From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1Pwx9i-0004pc-2X for garchives@archives.gentoo.org; Tue, 08 Mar 2011 13:41:10 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 445A8E0693; Tue, 8 Mar 2011 13:40:45 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id 295F1E0693 for ; Tue, 8 Mar 2011 13:40:44 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher ADH-CAMELLIA256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 0FE951B40AD for ; Tue, 8 Mar 2011 13:40:43 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id 5F1968006A for ; Tue, 8 Mar 2011 13:40:42 +0000 (UTC) From: "Alexey Shvetsov" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Alexey Shvetsov" Message-ID: Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/files/, sci-chemistry/ambertools/ X-VCS-Repository: proj/sci X-VCS-Files: sci-chemistry/ambertools/ambertools-1.4.ebuild sci-chemistry/ambertools/files/ambertools-1.4-bugfix_1-18.patch X-VCS-Directories: sci-chemistry/ambertools/files/ sci-chemistry/ambertools/ X-VCS-Committer: alexxy X-VCS-Committer-Name: Alexey Shvetsov X-VCS-Revision: fce91f0e433467027ef88ae12368ad1ba2cb72cf Date: Tue, 8 Mar 2011 13:40:42 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: X-Archives-Hash: 67ad0bef9d0057e894923b9263f63531 commit: fce91f0e433467027ef88ae12368ad1ba2cb72cf Author: Alexey Shvetsov gentoo org> AuthorDate: Tue Mar 8 13:40:18 2011 +0000 Commit: Alexey Shvetsov gentoo org> CommitDate: Tue Mar 8 13:40:18 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3Dfce91f0e [ambertools] apply upstream bugfixes --- sci-chemistry/ambertools/ambertools-1.4.ebuild | 1 + .../files/ambertools-1.4-bugfix_1-18.patch | 9025 ++++++++++++++= ++++++ 2 files changed, 9026 insertions(+), 0 deletions(-) diff --git a/sci-chemistry/ambertools/ambertools-1.4.ebuild b/sci-chemist= ry/ambertools/ambertools-1.4.ebuild index 9e1297e..fda14ee 100644 --- a/sci-chemistry/ambertools/ambertools-1.4.ebuild +++ b/sci-chemistry/ambertools/ambertools-1.4.ebuild @@ -52,6 +52,7 @@ pkg_setup() { } =20 src_prepare() { + epatch "${FILESDIR}/${P}-bugfix_1-18.patch" epatch "${FILESDIR}/${P}-gentoo.patch" cd AmberTools/src rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf= reduce ucpp-1.3 || die diff --git a/sci-chemistry/ambertools/files/ambertools-1.4-bugfix_1-18.pa= tch b/sci-chemistry/ambertools/files/ambertools-1.4-bugfix_1-18.patch new file mode 100644 index 0000000..2bc899b --- /dev/null +++ b/sci-chemistry/ambertools/files/ambertools-1.4-bugfix_1-18.patch @@ -0,0 +1,9025 @@ +diff -urN amber11.orig/AmberTools/src/gleap/leapsrc/plugins.cpp amber11/= AmberTools/src/gleap/leapsrc/plugins.cpp +--- amber11.orig/AmberTools/src/gleap/leapsrc/plugins.cpp 2010-03-31 07:= 05:14.000000000 +0400 ++++ amber11/AmberTools/src/gleap/leapsrc/plugins.cpp 2011-03-08 16:38:44= .000000000 +0300 +@@ -37,7 +37,7 @@ +=20 + amber::help_command g_help_command; + amber::add_command g_add_command2; +-amber::addions_command g_addions_command2; ++amber::addions_command g_addions_command2( "addions" ); + amber::addmap_command g_addpdbatommap_command2( "addpdbatommap" ); + amber::addmap_command g_addpdbresmap_command2( "addpdbresmap" ); + amber::null_command g_addatomtypes_command2( "addatomtypes" ); +diff -urN amber11.orig/AmberTools/src/gleap/mortsrc/ambfmt/parm.cpp ambe= r11/AmberTools/src/gleap/mortsrc/ambfmt/parm.cpp +--- amber11.orig/AmberTools/src/gleap/mortsrc/ambfmt/parm.cpp 2010-03-31= 07:05:14.000000000 +0400 ++++ amber11/AmberTools/src/gleap/mortsrc/ambfmt/parm.cpp 2011-03-08 16:3= 8:44.000000000 +0300 +@@ -110,7 +110,7 @@ + assert( tmp.size() =3D=3D 3 ); + atmvec as(tmp); + =20 +- angl_t an =3D angl_t::create( as[0], as[1], as[2] ); ++ angl_t an =3D angl_t::frcget( as[0], as[1], as[2] ); + set_les( an ); +=20 + atom_t pa1( *pff, as[0].get_i(TYPEID)-1 ); +@@ -277,6 +277,15 @@ + copy_dparm(pdihs[i], SCEE, di); + copy_dparm(pdihs[i], SCNB, di); + set_les( di ); ++ ++ /* ++ std::cout << as[0].get_s(NAME) << "-"; ++ std::cout << as[1].get_s(NAME) << "-"; ++ std::cout << as[2].get_s(NAME) << "-"; ++ std::cout << as[3].get_s(NAME) << " SCEE=3D" << di.= get_d(SCEE) << std::endl; ++ */ ++ ++ + } =20 + } + } +@@ -434,6 +443,8 @@ + parm_gbsa( *ai, gbtype ); + } +=20 ++ //std::cout << " atom parameter assigned." << std::endl; ++ + bonditer_t bi =3D mol.bond_begin(); + bonditer_t be =3D mol.bond_end(); + for( ; bi !=3D be; ++bi ) +@@ -441,6 +452,8 @@ + parm_bond( &ff, *bi ); + } +=20 ++ //std::cout << " bond parameter assigned." << std::endl; ++ + bool fw =3D fixed_water(); + ai =3D mol.atom_begin(); + ae =3D mol.atom_end(); +diff -urN amber11.orig/AmberTools/src/gleap/mortsrc/ambfmt/prep.cpp ambe= r11/AmberTools/src/gleap/mortsrc/ambfmt/prep.cpp +--- amber11.orig/AmberTools/src/gleap/mortsrc/ambfmt/prep.cpp 2010-03-31= 07:05:14.000000000 +0400 ++++ amber11/AmberTools/src/gleap/mortsrc/ambfmt/prep.cpp 2011-03-08 16:3= 8:44.000000000 +0300 +@@ -39,7 +39,7 @@ + resd_t r =3D resd_t::create( m ); + r.set_s(NAME, name); + r.set_s(TYPE, name.length()<3?name:name.substr(0,3)); +- ++ //std::cout << "Loading model " << name << std::endl; + // CORR/CHANGE, if CHANGE then sort line according=20 + // the first column, no supported any more. + string use_first_column; +@@ -55,9 +55,13 @@ + is >> cutoff; + is.ignore(MAX_LINE_WIDTH, '\n'); +=20 ++ vector crdlst; ++ vector nbrmap; ++ ++ // stacks + vector atoms; +- vector crds; + vector nunfills; ++ vector idxstack; +=20 + int head =3D 0; + int tail =3D 0; +@@ -71,7 +75,7 @@ + string name, type, chain; + ls >> name >> type >> chain; +=20 +- ++ //std::cout << " processing atom " << name << std::endl; + string curt; + vector terms; + while(ls >> curt) +@@ -96,22 +100,31 @@ + double angl =3D atof( terms[4].c_str() ); + double tors =3D atof( terms[5].c_str() ); + pchg =3D (terms.size()=3D=3D7) ? atof( terms[6].c_str() ) : 0.0; +- int len =3D crds.size(); +- if(len=3D=3D0) ++ if( idxstack.size()=3D=3D0 ) + { + pos =3D makevec(0.0, 0.0, 0.0); +- } +- else if(len=3D=3D1) +- { +- pos =3D zmatrix(crds[len-1], dist); +- } +- else if(len=3D=3D2) +- { +- pos =3D zmatrix(crds[len-1], dist, crds[len-2], angl); ++ crdlst.push_back( pos ); ++ nbrmap.push_back( -1 ); + } + else +- { +- pos =3D zmatrix(crds[len-1], dist, crds[len-2], ang= l, crds[len-3], tors); ++ { ++ int nbr1 =3D idxstack.back(); ++ int nbr2 =3D nbrmap[nbr1]; ++ int nbr3 =3D (nbr2=3D=3D-1) ? -1 : nbrmap[nbr2]; ++ if(nbr2=3D=3D-1) ++ { ++ pos =3D zmatrix(crdlst[nbr1], dist); ++ } ++ else if(nbr3=3D=3D-1) ++ { ++ pos =3D zmatrix(crdlst[nbr1], dist, crdlst[nbr2], angl); ++ } ++ else ++ { ++ pos =3D zmatrix(crdlst[nbr1], dist, crdlst[nbr2= ], angl, crdlst[nbr3], tors); ++ } ++ crdlst.push_back( pos ); ++ nbrmap.push_back( nbr1 ); + } + } +=20 +@@ -127,7 +140,7 @@ +=20 + if(atoms.size() > 0) + { +- assert( nunfills.size()=3D=3Dcrds.size() ); ++ assert( nunfills.size()=3D=3Didxstack.size() ); + bond_t::create(atom, atoms.back() ).set_i(ORDER, 1); + nunfills.back() -=3D 1; + } +@@ -145,7 +158,7 @@ +=20 + if( nunfills.size()>0 && nunfills.back()=3D=3D0 ) + { +- crds.pop_back(); ++ idxstack.pop_back(); + atoms.pop_back(); + nunfills.pop_back(); + } +@@ -153,7 +166,7 @@ + int nunfill =3D get_nunfill(chain); + if(nunfill > 0) + { +- crds.push_back(pos); ++ idxstack.push_back(crdlst.size()-1); + if(type !=3D "DU") + atoms.push_back(atom); + nunfills.push_back(nunfill); +diff -urN amber11.orig/AmberTools/src/gleap/mortsrc/capbox/addions.cpp a= mber11/AmberTools/src/gleap/mortsrc/capbox/addions.cpp +--- amber11.orig/AmberTools/src/gleap/mortsrc/capbox/addions.cpp 2010-03= -31 07:05:14.000000000 +0400 ++++ amber11/AmberTools/src/gleap/mortsrc/capbox/addions.cpp 2011-03-08 1= 6:38:44.000000000 +0300 +@@ -83,11 +83,82 @@ +=20 + void addions( molecule_t& m, const molecule_t& ion, int num_ion, do= uble shlext, double resolution ) + { ++ vector ionlst(num_ion, ion); + mort_ionee ionee(m); +- addions_core( ionee, ion, num_ion, shlext, resolution ); ++ addions_core( ionee, ionlst, shlext, resolution ); ++ m.cleanup(); + } +=20 +- void addions_core( ionee_i& ionee, const molecule_t& ion, int num_i= on, double shlext, double resolution ) ++ void addions( molecule_t& m, const molecule_t& ion1, int numion1, c= onst molecule_t& ion2, int numion2, double shlext, double resolution ) ++ { ++ vector ionlst; ++ int minnumion =3D std::min( numion1, numion2 ); ++ for( int i=3D0; i < minnumion; ++i ) ++ { ++ ionlst.push_back( ion1 ); ++ ionlst.push_back( ion2 ); ++ } ++ ++ int moreadd =3D std::max( numion1, numion2 ) - minnumion; ++ if( moreadd > 0 ) ++ { ++ const molecule_t* padd =3D (minnumion=3D=3Dnumion1) ? &ion2= : &ion1; ++ for( int i=3D0; i < moreadd; ++i ) ++ { ++ ionlst.push_back( *padd ); ++ } ++ } ++ =20 ++ mort_ionee ionee(m); ++ addions_core( ionee, ionlst, shlext, resolution ); ++ m.cleanup(); ++ } ++ ++ double get_ionvdwr( const molecule_t& ion ) ++ { ++ double r =3D get_vdwr( ion.atom_begin()->get_s(TYPE) ); ++ if( ion.natom() > 1 ) ++ { ++ std::cout << "Info: polyatomic ion, radius set to " << r*2.= 5 << " (2.5 times first atom)" << std::endl; ++ r *=3D 2.5; ++ } ++ return r; ++ } ++ ++ double get_minvdwr( const vector& ionlst ) ++ { ++ double minr =3D 1000.0; ++ int numion =3D ionlst.size(); ++ for( int i=3D0; i < numion; ++i ) ++ { ++ double r =3D get_ionvdwr( ionlst[i] ); ++ minr =3D std::min( r, minr ); ++ } ++ ++ if( numion > 5 ) ++ { ++ double f =3D exp( log(numion+1.0)/3.0 ); ++ if( f > 1.0 ) minr *=3D f; ++ } ++ ++ return minr; ++ } ++ ++ double get_maxvdwr( const vector& ionlst ) ++ { ++ double maxr =3D 0.0; ++ int numion =3D ionlst.size(); ++ for( int i=3D0; i < numion; ++i ) ++ { ++ double r =3D get_ionvdwr( ionlst[i] ); ++ maxr =3D std::max( r, maxr ); ++ } ++ ++ return maxr; ++ } ++ ++ ++ void addions_core( ionee_i& ionee, const vector& ionlst= , double shlext, double resolution ) + { + int natom =3D ionee.natom(); + int nresd =3D ionee.nresd(); +@@ -98,8 +169,8 @@ +=20 + if( solute_natom !=3D ionee.natom() ) + { +- std::cout << "Info: solute natom, total natom: " << solute_= natom << " " << natom << std::endl; +- std::cout << " solute nresd, total nresd: " << solute_= nresd << " " << nresd << std::endl; ++ std::cout << "Info: Number of solute atoms: " << solute_nat= om << ", total number of atoms: " << natom << std::endl; ++ std::cout << " Number of solute residues: " << solute_= nresd << ", total number of residues: " << nresd << std::endl; + } +=20 + vector& pcord =3D ionee.getcord(); +@@ -111,23 +182,12 @@ + minmaxpos( pcord, pmin, pmax, solute_natom ); +=20 + double max_radius =3D *std::max_element( pvdwr.begin(), pvdwr.e= nd() ); +- double ion_radius =3D get_vdwr( ion.atom_begin()->get_s(TYPE) )= ; +- if( ion.natom() > 1 ) +- { +- std::cout << "Info: polyatomic ion, radius set to " << ion_= radius*2.5 << " (2.5 times first atom)" << std::endl; +- ion_radius *=3D 2.5; +- } +- +- if( std::abs( charge(ion) ) < 0.1 ) +- { +- throw std::runtime_error( "Error: the ion you chose is in fact net= ural, thus add ion won't work" ); +- } ++ double ion_radius =3D get_maxvdwr( ionlst ); +=20 + double buffer =3D ion_radius + max_radius + shlext; + std::cout << "Info: rmax, rion, shell: " << max_radius << " " <= < ion_radius << " " << shlext << std::endl; +- +- std::cout << "Info: pmin: " << pmin[0] << " " << pmin[1] << " "= << pmin[2] << std::endl; +- std::cout << "Info: pmax: " << pmax[0] << " " << pmax[1] << " " << pma= x[2] << std::endl; ++ //std::cout << "Info: pmin: " << pmin[0] << " " << pmin[1] << "= " << pmin[2] << std::endl; ++ //std::cout << "Info: pmax: " << pmax[0] << " " << pmax[1] << " " << p= max[2] << std::endl; +=20 +=20 + pmin -=3D makevec(buffer, buffer, buffer); +@@ -151,9 +211,20 @@ + std::pair max =3D make_pair(-1e20, numvec(3)); + tree.calculate( capbox::elepot_t(&pcord[0], &pchrg[0], solute_n= atom), min, max ); +=20 +- for( int i=3D0; i < num_ion; ++i ) ++ int numion =3D ionlst.size(); ++ for( int i=3D0; i < numion; ++i ) + { +- numvec pos =3D charge(ion)>0 ? min.second : max.second; ++ if( std::abs( charge(ionlst[i]) ) < 0.1 ) ++ { ++ throw std::runtime_error( "Error: the ion you chose is in fact= netural, thus add ion won't work" ); ++ } ++ ++ std::cout << "min potential: " << min.first << " x,y,z: " = << min.second[0] << " " << min.second[1] << " " << min.second[2] << std::= endl; ++ std::cout << "max potential: " << max.first << " x,y,z: " = << max.second[0] << " " << max.second[1] << " " << max.second[2] << std::= endl; ++ ++ ++ ++ numvec pos =3D charge(ionlst[i])>0 ? min.second : max.secon= d; +=20 + if( nosolvent ) + { +@@ -161,8 +232,8 @@ + std::cout << "Info: new ion will be placed at: "; + std::cout << pos[0] << " " << pos[1] << " " << pos[2] = << " " << std::endl; +=20 +- numvec sft =3D pos - center(ion); +- ionee.insert_resd( ion, sft, -1 ); ++ numvec sft =3D pos - center(ionlst[i]); ++ ionee.insert_resd( ionlst[i], sft, -1 ); + } + else + { +@@ -171,19 +242,19 @@ + { + // solvent present, find the nearest solvent residu= e, use ion to replace it. + // besides the ion must be before solvent, after t= he solute +- numvec sft =3D pos - center(ion); +- ionee.insert_resd( ion, sft, solute_nresd+i ); ++ numvec sft =3D pos - center(ionlst[i]); ++ ionee.insert_resd( ionlst[i], sft, solute_nresd+i )= ; + ionee.remove_resd( rid ); + } + else + { + // no bump atom: insert residue directly, no need t= o delete solvent residue +- numvec sft =3D pos - center(ion); +- ionee.insert_resd( ion, sft, solute_nresd+i ); ++ numvec sft =3D pos - center(ionlst[i]); ++ ionee.insert_resd( ionlst[i], sft, solute_nresd+i )= ; + } + } +=20 +- if( i < num_ion-1 ) ++ if( i < numion-1 ) + { + // more ions to add: cut a sphere from the tree, make s= ure no overlapping + // the radius is 2*ion_radius, to avoid in the future i= on +@@ -193,7 +264,7 @@ +=20 + min.first =3D 1e20; + max.first =3D-1e20; +- tree.calculate(elepot_t(pos, charge(ion)), min, max); ++ tree.calculate(elepot_t(pos, charge(ionlst[i])), min, m= ax); + } + } +=20 +diff -urN amber11.orig/AmberTools/src/gleap/mortsrc/capbox/addions.hpp a= mber11/AmberTools/src/gleap/mortsrc/capbox/addions.hpp +--- amber11.orig/AmberTools/src/gleap/mortsrc/capbox/addions.hpp 2010-03= -31 07:05:14.000000000 +0400 ++++ amber11/AmberTools/src/gleap/mortsrc/capbox/addions.hpp 2011-03-08 1= 6:38:44.000000000 +0300 +@@ -91,7 +91,7 @@ +=20 + if( i !=3D m_natom ) + { +- throw std::runtime_error( "Error: there are atoms d= o not belong to any residue" ); ++ throw std::runtime_error( "Error: Atoms are present= that are part of no residue!" ); + } +=20 + m_pcord =3D &m_cord; +@@ -178,9 +178,11 @@ + vector m_type; + }; +=20 +- void addions_core( ionee_i& ionee, const molecule_t& ion, int nion,= double shlext, double resolution ); +-=20 ++ void addions_core( ionee_i& ionee, const vector& ionlst= , double shlext, double resolution ); ++ =20 + void addions( molecule_t& m, const molecule_t& ion, int nion, doubl= e shlext, double res ); ++ ++ void addions( molecule_t& m, const molecule_t& ion1, int numion1, c= onst molecule_t& ion2, int numion2, double shlext, double res ); + } +=20 + =20 +diff -urN amber11.orig/AmberTools/src/gleap/mortsrc/capbox/solvate.cpp a= mber11/AmberTools/src/gleap/mortsrc/capbox/solvate.cpp +--- amber11.orig/AmberTools/src/gleap/mortsrc/capbox/solvate.cpp 2010-03= -31 07:05:14.000000000 +0400 ++++ amber11/AmberTools/src/gleap/mortsrc/capbox/solvate.cpp 2011-03-08 1= 6:38:44.000000000 +0300 +@@ -126,13 +126,23 @@ + return cap.extent(); + } + =20 +- numvec solvatebox_core( solute_i& solute, const molecule_t& m, doub= le buffer, double closeness ) ++ numvec solvatebox_core( solute_i& solute, const molecule_t& m, doub= le buffer, double closeness, bool iso ) + { + funstack_t::push( "solvatebox" ); +=20 + numvec extent =3D regionlize( solute, true ); + extent +=3D scalar_numvec(extent.size(), 2*buffer); +=20 ++ if( iso ) ++ { ++ double extmax =3D std::max( extent[0], std::max(extent[1], = extent[2]) ); ++ extent[0] =3D extmax; ++ extent[1] =3D extmax; ++ extent[2] =3D extmax; ++ } ++ ++ ++ + box_region box( extent ); + out_solute inn( solute, closeness ); + solvate( solute, m, and_region(box, inn) ); +@@ -180,10 +190,10 @@ + mol.set_v( CAP, makevec(capcnt[0],capcnt[1],capcnt[2],caprad) )= ; + } +=20 +- void solvatebox(molecule_t& mol, const molecule_t& svt, double buff= er, double closeness) ++ void solvatebox(molecule_t& mol, const molecule_t& svt, double buff= er, double closeness, bool iso) + { + mort_solute solute(mol); +- numvec extent =3D solvatebox_core( solute, svt, buffer, closene= ss ); ++ numvec extent =3D solvatebox_core( solute, svt, buffer, closene= ss, iso ); + =20 + mol.set_i( SOLUTE, BOX ); + mol.set_v( BOX, makevec(extent[0], extent[1], extent[2], 90.0) = ); +diff -urN amber11.orig/AmberTools/src/gleap/mortsrc/capbox/solvate.hpp a= mber11/AmberTools/src/gleap/mortsrc/capbox/solvate.hpp +--- amber11.orig/AmberTools/src/gleap/mortsrc/capbox/solvate.hpp 2010-03= -31 07:05:14.000000000 +0400 ++++ amber11/AmberTools/src/gleap/mortsrc/capbox/solvate.hpp 2011-03-08 1= 6:38:44.000000000 +0300 +@@ -10,7 +10,7 @@ +=20 + numvec solvatecap_core( solute_i& solute, const molecule_t& m, cons= t numvec& capcnt, double caprad, double closeness ); + =20 +- numvec solvatebox_core( solute_i& solute, const molecule_t& m, doub= le buffer, double closeness ); ++ numvec solvatebox_core( solute_i& solute, const molecule_t& m, doub= le buffer, double closeness, bool iso ); + =20 + double solvateoct_core( solute_i& solute, const molecule_t& m, doub= le buffer, double closeness ); + =20 +@@ -18,7 +18,7 @@ + =20 + void solvatecap( molecule_t& mol, const molecule_t& svt, const numv= ec& capcnt, double caprad, double closeness ); + =20 +- void solvatebox( molecule_t& mol, const molecule_t& svt, double buf= fer, double closeness ); ++ void solvatebox( molecule_t& mol, const molecule_t& svt, double buf= fer, double closeness, bool iso ); + =20 + void solvateoct( molecule_t& mol, const molecule_t& svt, double buf= fer, double closeness ); + =20 +diff -urN amber11.orig/AmberTools/src/gleap/mortsrc/pdbent/atom.cpp ambe= r11/AmberTools/src/gleap/mortsrc/pdbent/atom.cpp +--- amber11.orig/AmberTools/src/gleap/mortsrc/pdbent/atom.cpp 2010-04-06= 04:38:00.000000000 +0400 ++++ amber11/AmberTools/src/gleap/mortsrc/pdbent/atom.cpp 2011-03-08 16:3= 8:44.000000000 +0300 +@@ -57,9 +57,9 @@ + { + funstack_t::push( "pdbent::write_atom" ); +=20 +- os << "ATOM "; ++ os << "ATOM "; +=20 +- write_iparm( os, atom, ID, "%5d" ); ++ write_iparm( os, atom, ID, "%6d" ); + =20 + write_atom_name( os, atom ); + =20 +@@ -102,7 +102,15 @@ + os << ' '; + } +=20 +- os << format( "%4d " ) % (atom.resd().relid()+1); ++ int rid =3D atom.resd().relid() + 1; ++ if( rid < 10000 ) ++ { ++ os << format( "%4d " ) % rid; ++ } ++ else ++ { ++ os << format( "%5d " ) % rid; ++ } + } + =20 + } // namespace pdbent +diff -urN amber11.orig/AmberTools/src/gleap/plugins/addions.cpp amber11/= AmberTools/src/gleap/plugins/addions.cpp +--- amber11.orig/AmberTools/src/gleap/plugins/addions.cpp 2010-03-31 07:= 05:14.000000000 +0400 ++++ amber11/AmberTools/src/gleap/plugins/addions.cpp 2011-03-08 16:38:44= .000000000 +0300 +@@ -4,15 +4,33 @@ +=20 + namespace amber + { ++ int get_numion( double dstchg, double ionchg ) ++ { ++ if( dstchg * ionchg >=3D 0 ) ++ { ++ throw std::runtime_error( "Error: molecule and ion are both= positive (or negative), can not make neutral" ); ++ } ++ =20 ++ return int( -dstchg/ionchg+0.5); ++ } ++ ++ + =20 +- addions_command::addions_command( ) +- :command_i( "addions" ) ++ addions_command::addions_command( const char* cmd ) ++ :command_i( cmd ) + { + } + =20 +- addions_command::addions_command( const string& dest, const string&= ion, int number ) +- :m_dest( dest ), m_ion( ion ), m_number( number ) ++ addions_command::addions_command( const string& dest, const string&= ion1, int numion1 ) ++ :m_dest( dest ), m_ion1( ion1 ), m_numion1( numion1 ) + { ++ m_runtyp =3D 1; ++ } ++ ++ addions_command::addions_command( const string& dest, const string&= ion1, int numion1, const string& ion2, int numion2 ) ++ :m_dest( dest ), m_ion1( ion1 ), m_numion1( numion1 ), m_ion2(i= on2), m_numion2(numion2) ++ { ++ m_runtyp =3D 2; + } + =20 + addions_command::~addions_command() +@@ -21,28 +39,42 @@ + =20 + bool addions_command::exec() + { ++ double shell_extent =3D 4.0; ++ double resolution =3D 1.0; + molecule_ptr pdst =3D content().get_mol( m_dest ); +- molecule_ptr pion =3D content().get_mol( m_ion ); +=20 +- if( m_number=3D=3D0 ) ++ if( m_runtyp=3D=3D1 ) + { +- double dstchg =3D charge( *pdst ); +- double ionchg =3D charge( *pion ); +- if( dstchg * ionchg >=3D 0 ) ++ molecule_ptr pion =3D content().get_mol( m_ion1 ); ++ if( m_numion1=3D=3D0 ) + { +- throw std::runtime_error( "Error: molecule and ion are = both positive (or negative), can not make neutral" ); ++ m_numion1 =3D get_numion( charge(*pdst), charge(*pion) = ); + } +- =20 +- m_number =3D int( -dstchg/ionchg+0.5); ++ ++ assert( pdst !=3D NULL && pion !=3D NULL ); ++ addions( *pdst, *pion, m_numion1, shell_extent, resolution)= ; + } +- =20 +- =20 +- assert( pdst !=3D NULL && pion !=3D NULL ); ++ else if( m_runtyp=3D=3D2 ) ++ { ++ molecule_ptr pion1 =3D content().get_mol( m_ion1 ); ++ molecule_ptr pion2 =3D content().get_mol( m_ion2 ); ++ if( m_numion1=3D=3D0 && m_numion2=3D=3D0 ) ++ { ++ throw std::runtime_error( "Error: while addions2, numio= n1 and numion2 cannot both be zero" ); ++ } +=20 +- double shell_extent =3D 4.0; +- double resolution =3D 1.0; ++ if( m_numion1=3D=3D0 ) ++ { ++ m_numion1 =3D get_numion( charge(*pdst)+m_numion2*charg= e(*pion2), charge(*pion1) ); ++ } ++ else if( m_numion2=3D=3D0 ) ++ { ++ m_numion2 =3D get_numion( charge(*pdst)+m_numion1*charg= e(*pion1), charge(*pion2) ); ++ } ++ ++ addions( *pdst, *pion1, m_numion1, *pion2, m_numion2, shell= _extent, resolution ); ++ } +=20 +- addions( *pdst, *pion, m_number, shell_extent, resolution); + return true; + } + =20 +@@ -53,22 +85,29 @@ +=20 + const char* addions_command::info( ) const + { +- return " usage: addion mol ion1 numIon1 "; ++ return " usage: addions mol ion1 numIon1 "; + } + =20 + shared_ptr< command_i > addions_command::clone( const vector< strin= g >& args ) const + { +- if( args.size()!=3D3 && args.size()!=3D4 ) ++ if( args.size()=3D=3D3 || args.size()=3D=3D4 ) + { +- throw std::runtime_error( "Error: wrong number of arguments= " ); ++ int numb =3D args.size()=3D=3D3 ? 0 : atoi(args[3].c_str())= ; ++ return shared_ptr< command_i >( new addions_command(args[1]= , args[2], numb) ); + } +=20 +- int numb =3D args.size()=3D=3D3 ? 0 : atoi(args[3].c_str()); +- =20 +- return shared_ptr< command_i >( new addions_command(args[1], ar= gs[2], numb) ); ++ if( args.size()=3D=3D6 ) ++ { ++ int nion1 =3D atoi( args[3].c_str() ); ++ int nion2 =3D atoi( args[5].c_str() ); ++ return shared_ptr< command_i >( new addions_command(args[1]= , args[2], nion1, args[4], nion2 ) ); ++ } ++ ++ throw std::runtime_error( "Error: Wrong number of arguments!" )= ; + } +=20 +- addions_command g_addions_command; ++ addions_command g_addions_command( "addions" ); ++ addions_command g_addions2_command( "addions2" ); + =20 + } // namespace amber +=20 +diff -urN amber11.orig/AmberTools/src/gleap/plugins/addions.hpp amber11/= AmberTools/src/gleap/plugins/addions.hpp +--- amber11.orig/AmberTools/src/gleap/plugins/addions.hpp 2010-03-31 07:= 05:14.000000000 +0400 ++++ amber11/AmberTools/src/gleap/plugins/addions.hpp 2011-03-08 16:38:44= .000000000 +0300 +@@ -11,10 +11,12 @@ + { + public: +=20 +- addions_command(); ++ addions_command( const char* cmdnam ); + =20 + addions_command( const string& dest, const string& ion, int num= ber ); +- =20 ++ ++ addions_command( const string& dest, const string& ion1, int nu= mion1, const string& ion2, int numion2 ); ++ + virtual ~addions_command(); + =20 + virtual bool exec(); +@@ -28,10 +30,12 @@ + private: +=20 + string m_dest; ++ string m_ion1; ++ int m_numion1; ++ string m_ion2; ++ int m_numion2; +=20 +- string m_ion; +- =20 +- int m_number; ++ int m_runtyp; + }; + =20 + } // namespace amber +diff -urN amber11.orig/AmberTools/src/gleap/plugins/check.cpp amber11/Am= berTools/src/gleap/plugins/check.cpp +--- amber11.orig/AmberTools/src/gleap/plugins/check.cpp 1970-01-01 03:00= :00.000000000 +0300 ++++ amber11/AmberTools/src/gleap/plugins/check.cpp 2011-03-08 16:38:44.0= 00000000 +0300 +@@ -0,0 +1,415 @@ ++#include ++#include "check.hpp" ++ ++namespace amber ++{ ++ void check_charge( const molecule_t& m ) ++ { ++ std::cout << "Checking charge: "; ++ double chg =3D charge( m ); ++ double dif =3D std::abs( chg - int(chg) ); ++ if( dif > 0.01 && dif < 0.99 ) ++ { ++ std::cout << std::endl; ++ std::cout << "Warning: non-integral total charge: " << chg = << std::endl; ++ } ++ else ++ { ++ std::cout << chg << ", OK!" << std::endl; ++ } ++ } ++ ++ void check_bond_length( const molecule_t& m, double lowcutoff, doub= le hghcutoff ) ++ { ++ std::cout << "Checking bond lengths: "; ++ bool ok =3D true; ++ bonditer_t bi =3D m.bond_begin(); ++ for( ; bi !=3D m.bond_end(); ++bi ) ++ { ++ atom_t a1 =3D atom_1st( *bi ); ++ atom_t a2 =3D atom_2nd( *bi ); ++ double ln =3D dist( a1, a2 ); ++ if( ln < lowcutoff || ln > hghcutoff ) ++ { ++ resd_t r1 =3D a1.resd(); ++ resd_t r2 =3D a2.resd(); ++ ok =3D false; ++ std::cout << std::endl; ++ std::cout << format("Warning: There is a bond of %4.2f = angstroms between: ") % ln; ++ std::cout << r1.get_s(NAME) << "." << a1.get_s(NAME) <<= " and "; ++ std::cout << r2.get_s(NAME) << "." << a2.get_s(NAME); ++ } ++ } ++ ++ if( ok ) ++ { ++ std::cout << "OK!" << std::endl; ++ } ++ else ++ { ++ std::cout << std::endl; ++ } ++ } ++ ++ void check_atom_distance( const molecule_t& m, double cutoff ) ++ { ++ std::cout << "Checking nonbonded atom contacts: "; ++ bool ok =3D true; ++ atomiter_t ai =3D m.atom_begin(); ++ for( ; ai !=3D m.atom_end(); ++ai ) ++ { ++ atomiter_t aj =3D ai + 1; ++ for( ; aj !=3D m.atom_end(); ++aj ) ++ { ++ if( bond_t::has(*ai, *aj) ) ++ { ++ continue; ++ } ++ ++ double d =3D dist( *ai, *aj ); ++ if( d < cutoff ) ++ { ++ ok =3D false; ++ resd_t r1 =3D ai->resd(); ++ resd_t r2 =3D aj->resd(); ++ std::cout << std::endl; ++ std::cout << format( "Warning: Close contact of %4.= 2f Angstroms between atoms ") % d; ++ std::cout << r1.get_s(NAME) << "." << ai->name() <<= " and "; ++ std::cout << r2.get_s(NAME) << "." << aj->name(); ++ } ++ } ++ } ++ ++ if( ok ) ++ { ++ std::cout << "OK!" << std::endl; ++ } ++ else ++ { ++ std::cout << std::endl; ++ } ++ } ++ ++ void check_atom_params( const molecule_t& m, const molecule_t& ff ) ++ { ++ std::cout << "Checking atom parameters: "; ++ bool ok =3D true; ++ atomiter_t ai =3D m.atom_begin(); ++ for( ; ai !=3D m.atom_end(); ++ai ) ++ { ++ string t =3D ai->type(); ++ if( !atom_t::has(ff, t) ) ++ { ++ ok =3D false; ++ std::cout << "Warning: could not find parameters for at= om: " << t << std::endl; ++ } ++ } ++ ++ if( ok ) ++ { ++ std::cout << "OK!" << std::endl; ++ } ++ else ++ { ++ std::cout << std::endl; ++ } ++ } ++ ++ void check_bond_params( const molecule_t& m, const molecule_t& ff ) ++ { ++ std::cout << "Checking bond parameters: "; ++ bool ok =3D true; ++ bonditer_t bi =3D m.bond_begin(); ++ for( ; bi !=3D m.bond_end(); ++bi ) ++ { ++ atom_t a1 =3D atom_1st( *bi ); ++ atom_t a2 =3D atom_2nd( *bi ); ++ string t1 =3D a1.type(); ++ string t2 =3D a2.type(); ++ ++ atom_t pa1(ff, -1), pa2(ff, -1); ++ ++ if( atom_t::get(ff, t1, pa1) && atom_t::get(ff, t2, pa2) ) ++ { ++ if( bond_t::has(pa1, pa2) ) ++ { ++ continue; ++ } ++ } ++ ++ ok =3D false; ++ std::cout << std::endl; ++ std::cout << "Warning: could not find parameters for bond "= << t1 << "-" << t2 << std::endl; ++ } ++ ++ if( ok ) ++ { ++ std::cout << "OK!" << std::endl; ++ } ++ else ++ { ++ std::cout << std::endl; ++ } ++ } ++ ++ void check_angl_params( const molecule_t& m, const molecule_t& ff ) ++ { ++ std::cout << "Checking angle parameters: "; ++ bool ok =3D true; ++ atomiter_t ai =3D m.atom_begin(); ++ for( ; ai !=3D m.atom_end(); ++ai ) ++ { ++ atomiter_t aj =3D ai->atom_begin(); ++ for( ; aj !=3D ai->atom_end(); ++aj ) ++ { ++ atomiter_t ak =3D aj + 1; ++ for( ; ak !=3D ai->atom_end(); ++ak ) ++ { ++ string t1 =3D ai->type(); ++ string t2 =3D aj->type(); ++ string t3 =3D ak->type(); ++ atom_t pa1(ff, -1); ++ atom_t pa2(ff, -1); ++ atom_t pa3(ff, -1); ++ if( atom_t::get(ff, t1, pa1) && atom_t::get(ff, t2,= pa2) && atom_t::get(ff, t3, pa3) ) ++ { ++ if( angl_t::has(pa2, pa1, pa3) ) ++ { ++ continue; ++ } ++ } ++ ++ ok =3D false; ++ std::cout << std::endl; ++ std::cout << "Warning: could not find parameters fo= r angle " << t2 << "-" << t1 << "-" << t3; ++ } ++ } ++ } ++ ++ if( ok ) ++ { ++ std::cout << "OK!" << std::endl; ++ } ++ else ++ { ++ std::cout << std::endl; ++ } ++ } ++ ++ check_command::check_command() ++ : command_i( "check" ) ++ { ++ } ++ ++ check_command::check_command( bool checkmolcharge, bool checkatomp= arams, ++ bool checkbondparams, bool checkangle= params, ++ bool checkbondlength, bool checkatomc= lashes, ++ const string& molnam ) ++ : m_checkmolcharge(checkmolcharge), m_checkatomparams(checkatom= params), ++ m_checkbondparams(checkbondparams), m_checkangleparams(checkang= leparams), ++ m_checkbondlength(checkbondlength), m_checkatomclashes(checkato= mclashes), ++ m_molnam( molnam ) ++ { ++ } ++ ++ check_command::~check_command( ) ++ { ++ } ++ ++ bool check_command::exec( ) ++ { ++ int ndot =3D std::count( m_molnam.begin(), m_molnam.end(), '.' = ); ++ if( ndot !=3D 0 ) ++ { ++ throw std::runtime_error( "Error: Arguments, other than fla= gs, must be units!" ); ++ } ++ =20 ++ std::cout << "Checking unit \"" << m_molnam << "\"" << std::end= l; ++ ++ molecule_ptr pmol =3D content().get_mol( m_molnam ); ++ molecule_ptr parm =3D content().get_mol( "_amberffp" ); ++ ++ if (m_checkmolcharge =3D=3D true) ++ { ++ check_charge( *pmol ); ++ } ++=09 ++ if (m_checkatomparams =3D=3D true) ++ { ++ check_atom_params( *pmol, *parm ); ++ } ++ =20 ++ if (m_checkbondparams =3D=3D true) ++ { ++ check_bond_params( *pmol, *parm ); ++ } ++ =20 ++ if (m_checkangleparams =3D=3D true) ++ { ++ check_angl_params( *pmol, *parm ); ++ } ++ =20 ++ if (m_checkbondlength =3D=3D true) ++ { ++ check_bond_length( *pmol, 0.5, 3.0 ); ++ } ++ =20 ++ if (m_checkatomclashes =3D=3D true) ++ { ++ check_atom_distance( *pmol, 1.5 ); ++ } ++ =20 ++ return true; ++ } ++ ++ void check_command::undo() ++ { ++ } ++ ++ const char* check_command::info() const ++ { ++ return "check unit"; ++ } ++ ++ command_ptr check_command::clone( const vector< string >& args ) co= nst ++ { ++ bool checkall =3D false; ++ bool checkmolcharge =3D false; ++ bool checkatomparams =3D false; ++ bool checkbondparams =3D false; ++ bool checkangleparams =3D false; ++ bool checkbondlength =3D false; ++ bool checkatomclashes =3D false; ++ bool nocheckatomclashes =3D false; ++ =20 ++ std::string unit =3D ""; ++ =20 ++ int i; ++ =20 ++ //if( args.size()!=3D2 ) ++ //{ ++ // throw std::runtime_error( "Error: Wrong number of argumen= ts!" ); ++ //} ++ =20 ++ for (i =3D 1; i < args.size(); i++) ++ { ++ if (args[i] =3D=3D "-charge") ++ { ++ checkmolcharge =3D true; ++ std::cout << "charge check requested" << std::endl; ++ } ++ else if (args[i] =3D=3D "-atomparams") ++ { ++ checkatomparams =3D true; ++ std::cout << "atom parameter check requested" << std::e= ndl; ++ } ++ else if (args[i] =3D=3D "-bondparams") ++ { ++ checkbondparams =3D true; ++ std::cout << "bond parameter check requested" << std::e= ndl; ++ } ++ else if (args[i] =3D=3D "-angleparams") ++ { ++ checkangleparams =3D true; ++ std::cout << "angle parameter check requested" << std::= endl; ++ } ++ else if (args[i] =3D=3D "-bondlength") ++ { ++ checkbondlength =3D true; ++ std::cout << "bond length check requested" << std::endl= ; ++ } ++ else if (args[i] =3D=3D "-clashes") ++ { ++ if (nocheckatomclashes =3D=3D true) ++ { ++ throw std::runtime_error("Error: can't use -clashes= and -noclashes together!"); ++ } ++ =20 ++ checkatomclashes =3D true; ++ std::cout << "atom proximity (clash) check requested" <= < std::endl; ++ } ++ else if (args[i] =3D=3D "-noclashes") ++ { ++ if (checkatomclashes =3D=3D true) ++ { ++ throw std::runtime_error("Error: can't use -clashes= and -noclashes together!"); ++ } ++ if (checkall =3D=3D true) ++ { ++ throw std::runtime_error("Error: can't use -all and= -noclashes together!"); ++ } ++ =20 ++ nocheckatomclashes =3D true; ++ // Set everything else, too ++ checkmolcharge =3D true; ++ checkatomparams =3D true; ++ checkbondparams =3D true; ++ checkangleparams =3D true; ++ checkbondlength =3D true; ++ checkatomclashes =3D false; ++ checkall =3D false; ++ std::cout << "all except atom proximity (clash) check r= equested" << std::endl; ++ } ++ else if (args[i] =3D=3D "-all") ++ { ++ if (nocheckatomclashes =3D=3D true) ++ { ++ throw std::runtime_error("Error: can't use -all and= -noclashes together!"); ++ } ++ =20 ++ checkall =3D true; ++ } ++ else if (args[i].substr(0,1) =3D=3D "-") ++ { ++ throw std::runtime_error("Error: in check, unrecognised= flag: " + args[i] + "\n" ++ + " Allowed flags:" + "= \n" ++ + " -charge" + "= \n" ++ + " -atomparams" + "= \n" ++ + " -bondparams" + "= \n" ++ + " -angleparams" + "= \n" ++ + " -bondlength" + "= \n" ++ + " -clashes" + "= \n" ++ + " -noclashes" + "= \n" ++ + " -all" = ); ++ } ++ else if (unit =3D=3D "") ++ { ++ unit =3D args[i]; ++ } ++ else ++ { ++ throw std::runtime_error("Error: Too many arguments!"); ++ } ++ } ++ =20 ++ if (unit =3D=3D "") ++ { ++ throw std::runtime_error("Error: A unit must be supplied as= an argument!"); ++ } ++ =20 ++ // If everything is false except possibly checkall (whose truth ++ // or falsity is irrelevant), we want to check everything ++ if (checkmolcharge =3D=3D false && checkatomparams =3D=3D false ++ && checkbondparams =3D=3D false && checkangleparams =3D=3D fal= se ++ && checkbondlength =3D=3D false && checkatomclashes =3D=3D fal= se ++ && nocheckatomclashes =3D=3D false) ++ { ++ checkmolcharge =3D true; ++ checkatomparams =3D true; ++ checkbondparams =3D true; ++ checkangleparams =3D true; ++ checkbondlength =3D true; ++ checkatomclashes =3D true; ++ std::cout << "all checks requested" << std::endl; ++ } ++ ++ return shared_ptr< command_i >( new check_command(checkmolcharg= e, checkatomparams, ++ checkbondpara= ms, checkangleparams, ++ checkbondleng= th, checkatomclashes, ++ unit ) ); ++ } ++ ++} // namespace amber ++ ++amber::check_command g_check_command; ++ +diff -urN amber11.orig/AmberTools/src/gleap/plugins/check.hpp amber11/Am= berTools/src/gleap/plugins/check.hpp +--- amber11.orig/AmberTools/src/gleap/plugins/check.hpp 1970-01-01 03:00= :00.000000000 +0300 ++++ amber11/AmberTools/src/gleap/plugins/check.hpp 2011-03-08 16:38:44.0= 00000000 +0300 +@@ -0,0 +1,49 @@ ++#ifndef GLEAP_PLUGINS_CHECK_HPP ++#define GLEAP_PLUGINS_CHECK_HPP ++ ++#include ++ ++namespace amber ++{ ++ ++ using namespace mort; ++ ++ class check_command : public command_i ++ { ++ public: ++ ++ check_command(); ++ ++ check_command( bool checkmolcharge, bool checkatomparams, ++ bool checkbondparams, bool checkangleparams, ++ bool checkbondlength, bool checkatomclashes, ++ const string& molnam ); ++ ++ virtual ~check_command(); ++ ++ virtual bool exec(); ++ ++ virtual void undo(); ++ ++ virtual const char* info( ) const; ++ ++ virtual shared_ptr< command_i > clone( const vector& ar= gs ) const; ++ ++ private: ++ ++ bool m_checkmolcharge; ++ bool m_checkatomparams; ++ bool m_checkbondparams; ++ bool m_checkangleparams; ++ bool m_checkbondlength; ++ bool m_checkatomclashes; ++ string m_molnam; ++ ++ }; ++ ++} // namespace amber ++ ++ ++ ++#endif ++ +diff -urN amber11.orig/AmberTools/src/gleap/plugins/loadpdb.cpp amber11/= AmberTools/src/gleap/plugins/loadpdb.cpp +--- amber11.orig/AmberTools/src/gleap/plugins/loadpdb.cpp 2010-03-31 07:= 05:14.000000000 +0400 ++++ amber11/AmberTools/src/gleap/plugins/loadpdb.cpp 2011-03-08 16:38:44= .000000000 +0300 +@@ -31,28 +31,29 @@ + throw std::runtime_error( "Error: file " + m_file + " doesn= 't exist" ); + } +=20 +- + molecule_ptr pmol( new molecule_t() ); +=20 + read_pdb( is, *pmol ); +=20 + string disulf =3D "auto"; + mortenv().get_s("disulfide", disulf); +- console_t* pcon =3D (disulf=3D=3D"auto") ? NULL : console().get= (); ++ if( disulf!=3D"off" ) ++ { ++ console_t* pcon =3D (disulf=3D=3D"auto") ? NULL : console()= .get(); +=20 +- double disulfcut =3D 2.1; +- string tmp; +- if( mortenv().get_s("disulfcut", tmp) ) +- { +- disulfcut =3D atof( tmp.c_str() ); +- } ++ double disulfcut =3D 2.1; ++ string tmp; ++ if( mortenv().get_s("disulfcut", tmp) ) ++ { ++ disulfcut =3D atof( tmp.c_str() ); ++ } +=20 +- disulfide( *pmol, disulfcut, pcon ); ++ disulfide( *pmol, disulfcut, pcon ); ++ } +=20 + namemap_ptr nmap =3D content().get_nmap( "_namemap" ); + if( nmap !=3D NULL ) + { +-=20 + if( m_action=3D=3D"loadpdb" ) + { + mdlize_mdb( *pmol, content() ); +diff -urN amber11.orig/AmberTools/src/gleap/plugins/merge.cpp amber11/Am= berTools/src/gleap/plugins/merge.cpp +--- amber11.orig/AmberTools/src/gleap/plugins/merge.cpp 2010-03-31 07:05= :14.000000000 +0400 ++++ amber11/AmberTools/src/gleap/plugins/merge.cpp 2011-03-08 16:38:44.0= 00000000 +0300 +@@ -241,6 +241,12 @@ +=20 +=20 + morf_t resd =3D merge(*pmol, *pseg, -1); ++ if( i=3D=3D1 ) ++ { ++ // for the first residue. the head atom need to be unse= t for counting nunit in topology. ++ resd.set_i(HEAD, 0); ++ } ++ + resd.get_i(HEAD, head); +=20 + if( m_action =3D=3D "sequence" && i > 1) +diff -urN amber11.orig/AmberTools/src/gleap/plugins/set.cpp amber11/Ambe= rTools/src/gleap/plugins/set.cpp +--- amber11.orig/AmberTools/src/gleap/plugins/set.cpp 2010-03-31 07:05:1= 4.000000000 +0400 ++++ amber11/AmberTools/src/gleap/plugins/set.cpp 2011-03-08 16:38:44.000= 000000 +0300 +@@ -4,6 +4,29 @@ +=20 + namespace amber + { ++ vector split( const string& a ) ++ { ++ size_t bgn =3D a.find( '{' ); ++ if( bgn=3D=3Dstring::npos ) bgn =3D 0; ++ else bgn =3D bgn + 1; ++ ++ size_t end =3D a.rfind( '}' ); ++ if( end=3D=3Dstring::npos ) end =3D a.length(); ++ ++ vector result; ++ std::istringstream is( a.substr(bgn, end - bgn) ); ++ string s; ++ while( is >> s ) ++ { ++ result.push_back( s ); ++ } ++ ++ return result; ++ } ++ ++ ++ ++ + numvec atov(const string& a, int len) + { + std::istringstream is(a); +@@ -98,9 +121,23 @@ + } + else if( parm =3D=3D "box" ) + { ++ numvec box(4); + obj.set_i(SOLUTE, BOX); +- obj.set_v(BOX, atov4d(value) ); +- return true; ++ vector itmlst =3D split( value ); ++ if( itmlst.size()=3D=3D3 || itmlst.size()=3D=3D4 ) ++ { ++ box[0] =3D atof( itmlst[0].c_str() ); ++ box[1] =3D atof( itmlst[1].c_str() ); ++ box[2] =3D atof( itmlst[2].c_str() ); ++ box[3] =3D (itmlst.size()=3D=3D4) ? atof(itmlst[3].c_st= r()) : 90.0; ++ obj.set_v(BOX, box); ++ return true; ++ } ++ else ++ { ++ std::cout << "Error: cannot understand box value: " << = value << std::endl; ++ return false; ++ } + } + else if( parm =3D=3D "cap" ) + { +diff -urN amber11.orig/AmberTools/src/gleap/plugins/solvate.cpp amber11/= AmberTools/src/gleap/plugins/solvate.cpp +--- amber11.orig/AmberTools/src/gleap/plugins/solvate.cpp 2010-03-31 07:= 05:14.000000000 +0400 ++++ amber11/AmberTools/src/gleap/plugins/solvate.cpp 2011-03-08 16:38:44= .000000000 +0300 +@@ -11,9 +11,9 @@ + } + =20 + solvate_command::solvate_command( const string& action, const strin= g& solute, const string& solvent,=20 +- const string& center, const strin= g& extent, double closeness ) ++ const string& center, const strin= g& extent, double closeness, bool iso ) + : m_action( action ), m_solute( solute ), m_center( center ), m= _solvent( solvent ), +- m_extent( extent ), m_closeness( closeness ) ++ m_extent( extent ), m_closeness( closeness ), m_iso(iso) + { + } + =20 +@@ -33,7 +33,7 @@ + { + double length =3D atof( m_extent.c_str() ); + =20 +- solvatebox( *psolute, *psolvent, length, m_closeness ); ++ solvatebox( *psolute, *psolvent, length, m_closeness, m_iso= ); +=20 + return true; + } +@@ -103,7 +103,48 @@ +=20 + shared_ptr< command_i > solvate_command::clone( const vector< strin= g >& args ) const + { +- if( args[0]=3D=3D"solvatebox" || args[0]=3D=3D"solvateshell" ||= args[0]=3D=3D"solvateoct" ) ++ if( args[0]=3D=3D"solvatebox" ) ++ { ++ bool iso =3D false; ++ double closeness =3D 1.0; ++ if( args.size()=3D=3D4 ) ++ { ++ iso =3D false; ++ closeness =3D 1.0; ++ } ++ else if( args.size()=3D=3D5 ) ++ { ++ if( args[4]=3D=3D"iso" ) ++ { ++ iso =3D true; ++ closeness =3D 1.0; ++ } ++ else ++ { ++ iso =3D false; ++ closeness =3D atof( args[4].c_str() ); ++ } ++ } ++ else if( args.size()=3D=3D6 ) ++ { ++ if( args[5] !=3D "iso" ) ++ { ++ throw std::runtime_error( "Error: cannot understand= argument: " + args[5] ); ++ } ++ ++ iso =3D true; ++ closeness =3D atof( args[4].c_str() ); ++ } ++ else ++ { ++ throw std::runtime_error( "Error: wrong number of argum= ent." ); ++ } ++ ++ return shared_ptr( new solvate_command(args[0], = args[1], args[2], "", args[3], closeness, iso) ); ++ } ++ ++ ++ if( args[0]=3D=3D"solvateshell" || args[0]=3D=3D"solvateoct" ) + { + if( args.size()!=3D4 && args.size()!=3D5 ) + { +@@ -111,7 +152,7 @@ + } +=20 + double closeness =3D (args.size()=3D=3D4) ? 1.0 : atof( args[4].c_= str() );=20 +- return shared_ptr< command_i >( new solvate_command( args[0= ], args[1], args[2], "", args[3], closeness ) ); ++ return shared_ptr( new solvate_command(args[0], = args[1], args[2], "", args[3], closeness, false) ); + } + =20 + assert( args[0] =3D=3D "solvatecap" ); +@@ -122,7 +163,7 @@ + } + =20 + double closeness =3D (args.size()=3D=3D5) ? 1.0 : atof( args[5]= .c_str() );=20 +- return shared_ptr< command_i >( new solvate_command( args[0], a= rgs[1], args[2], args[3], args[4], closeness ) ); ++ return shared_ptr< command_i >( new solvate_command( args[0], a= rgs[1], args[2], args[3], args[4], closeness,false) ); + } + =20 + } // namespace amber +diff -urN amber11.orig/AmberTools/src/gleap/plugins/solvate.hpp amber11/= AmberTools/src/gleap/plugins/solvate.hpp +--- amber11.orig/AmberTools/src/gleap/plugins/solvate.hpp 2010-03-31 07:= 05:14.000000000 +0400 ++++ amber11/AmberTools/src/gleap/plugins/solvate.hpp 2011-03-08 16:38:44= .000000000 +0300 +@@ -13,7 +13,7 @@ +=20 + solvate_command( const string& type ); + =20 +- solvate_command( const string& action, const string& solute, co= nst string& solvent, const string& center, const string& extent, double c= loseness ); ++ solvate_command( const string& action, const string& solute, co= nst string& solvent, const string& center, const string& extent, double c= loseness, bool iso ); + =20 + virtual ~solvate_command( ); + =20 +@@ -38,6 +38,8 @@ + string m_extent; +=20 + double m_closeness; ++ ++ bool m_iso; + }; +=20 + } // namespace amber +diff -urN amber11.orig/AmberTools/src/leap/src/leap/basics.c amber11/Amb= erTools/src/leap/src/leap/basics.c +--- amber11.orig/AmberTools/src/leap/src/leap/basics.c 2010-03-31 07:05:= 15.000000000 +0400 ++++ amber11/AmberTools/src/leap/src/leap/basics.c 2011-03-08 16:38:44.00= 0000000 +0300 +@@ -462,7 +462,7 @@ + SmPMallocList =3D mPMem; + =20 + sTrailer =3D ((char*)mPMem)+sizeof(MEMHEADER)+lSize; +- memcpy( sTrailer, mPMem->sCheck, TRAILERLEN ); ++ memmove( sTrailer, mPMem->sCheck, TRAILERLEN ); + =20 + return ((char*)mPMem) + sizeof(MEMHEADER); + } +@@ -528,7 +528,7 @@ + if ( mPMem =3D=3D NULL ) { + DFATAL(( "Could not malloc in REALLOC: %s\n", strerror(errno) )= ); + } +- memcpy( mPMem, mPPrevious,=20 ++ memmove( mPMem, mPPrevious,=20 + MIN( lSize, mPPrevious->lSize) + sizeof(MEMHEADER)+TRAILERLE= N ); + =20 + strcpy( mPPrevious->sCheck, FREESTR ); +@@ -540,7 +540,8 @@ + /* Fill the trailer */ + =20 + sTrailer =3D ((char*)mPMem)+sizeof(MEMHEADER)+lSize; +- strcpy( sTrailer, mPMem->sCheck ); ++ memmove( sTrailer, mPMem->sCheck, strlen(mPMem->sCheck) ); ++ sTrailer[strlen(mPMem->sCheck)]=3D'\0'; + =20 + return ((char*)mPMem) + sizeof(MEMHEADER); + } +diff -urN amber11.orig/AmberTools/src/leap/src/leap/database.c amber11/A= mberTools/src/leap/src/leap/database.c +--- amber11.orig/AmberTools/src/leap/src/leap/database.c 2010-03-31 07:0= 5:15.000000000 +0400 ++++ amber11/AmberTools/src/leap/src/leap/database.c 2011-03-08 16:38:44.= 000000000 +0300 +@@ -594,6 +594,7 @@ + sStripString( char *sLine, char *sStr ) + { + char c, *sCur, *sStart; ++int mylength; +=20 + sCur =3D sLine; + sStart =3D sStr; +@@ -615,8 +616,10 @@ + (*sStr++) =3D c; + } while ( (*sCur) !=3D '\0' ); + *sStr =3D '\0'; +- strcpy( sLine, sCur ); +- =20 ++ mylength=3Dstrlen(sCur); ++ //strcpy( sLine, sCur ); ++ memmove(sLine, sCur, mylength); ++ sLine[mylength]=3D'\0'; + return(sStart); + } +=20 +diff -urN amber11.orig/AmberTools/src/leap/src/leap/sort.c amber11/Amber= Tools/src/leap/src/leap/sort.c +--- amber11.orig/AmberTools/src/leap/src/leap/sort.c 2010-03-31 07:05:15= .000000000 +0400 ++++ amber11/AmberTools/src/leap/src/leap/sort.c 2011-03-08 16:38:44.0000= 00000 +0300 +@@ -217,9 +217,9 @@ + /* If false then swap it with the bottom of the false */ + /* group, and leave the current pointer where it is */ +=20 +- memcpy( PSwapBuffer, PCur, iElementSize ); +- memcpy( PCur, PTop, iElementSize ); +- memcpy( PTop, PSwapBuffer, iElementSize ); ++ memmove( PSwapBuffer, PCur, iElementSize ); ++ memmove( PCur, PTop, iElementSize ); ++ memmove( PTop, PSwapBuffer, iElementSize ); +=20 + PTop =3D (char*)PTop - iElementSize; + iBottomFalse--; +diff -urN amber11.orig/AmberTools/src/leap/src/leap/stringExtra.c amber1= 1/AmberTools/src/leap/src/leap/stringExtra.c +--- amber11.orig/AmberTools/src/leap/src/leap/stringExtra.c 2010-03-31 0= 7:05:15.000000000 +0400 ++++ amber11/AmberTools/src/leap/src/leap/stringExtra.c 2011-03-08 16:38:= 44.000000000 +0300 +@@ -130,10 +130,13 @@ + sRemoveLeadingSpaces( char *sLine ) + { + char *sTemp; +- ++int mylength; + sTemp =3D sLine; + while ( (*sTemp=3D=3D' ') && ( *sTemp!=3D'\0' )) sTemp++; +- strcpy( sLine, sTemp ); ++ mylength=3Dstrlen(sTemp); ++ //strcpy( sLine, sTemp ); ++ memmove(sLine, sTemp, mylength); ++ sLine[mylength]=3D'\0'; + return(sLine); + } +=20 +@@ -152,6 +155,7 @@ + sRemoveFirstString( char *sLine, char *sHead ) + { + char *sTemp; ++int mylength; +=20 + sTemp =3D sLine; + while ( (*sTemp!=3D' ') && ( *sTemp!=3D'\0' )) sTemp++; +@@ -163,7 +167,11 @@ + *sTemp =3D '\0'; + strcpy( sHead, sLine ); + sTemp++; +- strcpy( sLine, sTemp ); ++ mylength=3Dstrlen(sTemp); ++ //strcpy( sLine, sTemp ); ++ memmove(sLine, sTemp, mylength); ++ sLine[mylength]=3D'\0'; ++ =20 + } +=20 +=20 +diff -urN amber11.orig/AmberTools/src/leap/src/leap/xaCommand.c amber11/= AmberTools/src/leap/src/leap/xaCommand.c +--- amber11.orig/AmberTools/src/leap/src/leap/xaCommand.c 2010-03-31 07:= 05:15.000000000 +0400 ++++ amber11/AmberTools/src/leap/src/leap/xaCommand.c 2011-03-08 16:38:44= .000000000 +0300 +@@ -837,7 +837,7 @@ + * at the top of the list + */ + qsort( saPNames, iNumber, sizeof(STRING),=20 +- (int (*) (void *, void *) )ziXACCompareTwoDirectoryEntries ); ++ (int (*) (const void *, const void *) )ziXACCompareTwoDirectoryEntrie= s ); +=20 + /* + * Reformulate as an array of pointers to char +diff -urN amber11.orig/AmberTools/src/pbsa/pb_init.f amber11/AmberTools/= src/pbsa/pb_init.f +--- amber11.orig/AmberTools/src/pbsa/pb_init.f 2010-03-31 07:05:15.00000= 0000 +0400 ++++ amber11/AmberTools/src/pbsa/pb_init.f 2011-03-08 16:38:44.000000000 = +0300 +@@ -153,6 +153,7 @@ + =20 + integer ires, iatm, jatm, maxmax, ic, i, j, jp, idum + integer alloc_err(64) ++ _REAL_ maxnbr_l, maxnba_l + _REAL_ rinchk + _REAL_ ucrgh(natom), ucrga(natom) + character (len=3D4) :: residue, resid(natom) +@@ -207,16 +208,24 @@ + =20 + ! allocate pb nblists + =20 +- maxnba =3D natom * ( sqrt( max(cutnb,cutsa,cutfd) ) )**3 / 3.0d0 +- maxnbr =3D natom * ( sqrt( cutres ) + 3.0d0 )**3 / 3.0d0 ++ maxnba_l =3D dble(natom) * ( sqrt( max(cutnb,cutsa,cutfd) ) )**3 / 3= .0d0 ++ maxnbr_l =3D dble(natom) * ( sqrt( cutres ) + 3.0d0 )**3 / 3.0d0 + if ( natom >=3D 65536 ) then + write(6,'(a)') "PB Warnning: natom**2 exceeds integer limit (2147= 483647)." + maxmax =3D 2147483647 + else + maxmax =3D ceiling(dble(natom)/2*dble(natom)) +- endif +- if ( maxnba > maxmax ) maxnba =3D maxmax +- if ( maxnbr > maxmax ) maxnbr =3D maxmax ++ end if ++ if ( maxnbr_l > maxmax ) then ++ maxnbr =3D maxmax ++ else ++ maxnbr =3D int(maxnbr_l) ++ end if ++ if ( maxnba_l > maxmax ) then ++ maxnba =3D maxmax ++ else ++ maxnba =3D int(maxnba_l) ++ end if +=20 + allocate( iar1pb (6,0:natom), stat =3D alloc_err(24) ) + allocate( iprshrt( maxnba ), stat =3D alloc_err(25) ) +diff -urN amber11.orig/AmberTools/src/ptraj/actions.c amber11/AmberTools= /src/ptraj/actions.c +--- amber11.orig/AmberTools/src/ptraj/actions.c 2010-03-31 07:05:16.0000= 00000 +0400 ++++ amber11/AmberTools/src/ptraj/actions.c 2011-03-08 16:38:44.000000000= +0300 +@@ -3655,6 +3655,8 @@ + { + action->mask =3D processAtomMask("*", action->state); + } ++ if (action->mask=3D=3DNULL)=20 ++ return INVALID_ARGUMENTS_RETURN_CODE; + /* Create a new "substate" trajInfo->state containing only some= atoms: */ + modifyStateByMask(&trajInfo->state, &action->state, action->mas= k, 0); + trajInfo->atoms =3D trajInfo->state->atoms; +@@ -16406,6 +16408,10 @@ + residues[i].antiparallelSheetProb =3D 0;=20 + residues[i].turnProb =3D 0; + residues[i].isActive =3D 0; ++ residues[i].H=3D-1; ++ residues[i].C=3D-1; ++ residues[i].N=3D-1; ++ residues[i].O=3D-1; + } + actRes =3D 0; + for (i =3D 0; i < action->state->atoms; i++) { +diff -urN amber11.orig/AmberTools/src/ptraj/cluster.c amber11/AmberTools= /src/ptraj/cluster.c +--- amber11.orig/AmberTools/src/ptraj/cluster.c 2010-03-31 07:05:16.0000= 00000 +0400 ++++ amber11/AmberTools/src/ptraj/cluster.c 2011-03-08 16:38:44.000000000= +0300 +@@ -4041,7 +4041,7 @@ + OutputTrajInfo =3D (trajectoryInfo*)action->carg2; + } +=20 +- if (!FirstOutputFlag) ++ if (FirstOutputFlag=3D=3DNULL) + { + FirstOutputFlag =3D (int*)SafeMalloc(__FILE__, __LINE__, sizeof(i= nt) * This->ClusterCount); + memset(FirstOutputFlag, 1, sizeof(int) * This->ClusterCount); +@@ -4089,7 +4089,7 @@ + * to avoid crashing out if we hit the OS-level file-size limit:= =20 + */ + FileNumber[ClusterIndex] =3D FileNumber[ClusterIndex] + 1; +- fclose(OutputFiles[ClusterIndex]); ++ safe_fclose(OutputFiles[ClusterIndex]); + FirstOutputFlag[ClusterIndex] =3D 1; + FirstFlag =3D 1; =20 + } +diff -urN amber11.orig/AmberTools/src/ptraj/io.c amber11/AmberTools/src/= ptraj/io.c +--- amber11.orig/AmberTools/src/ptraj/io.c 2010-03-31 07:05:16.000000000= +0400 ++++ amber11/AmberTools/src/ptraj/io.c 2011-03-08 16:38:44.000000000 +030= 0 +@@ -673,6 +673,107 @@ + } + } +=20 ++/* gzipFileSize() ++ * DRR: Return the uncompressed size in bytes of gzipped file by peekin= g=20 ++ * at the last 4 bytes. ++ * NOTE: long long int should be equivalent to off_t.=20 ++ */ ++long long int gzipFileSize(char *filename) { ++ FILE *infile; ++ unsigned char b1,b2,b3,b4; ++ long long int val,temp; ++ ++ if (filename=3D=3DNULL) return -1; ++ if ( (infile =3D fopen(filename,"rb"))=3D=3DNULL ) { ++ fprintf(stdout,"Error: gzipFileSize: Could not open %s for reading.= \n",filename); ++ return -1; ++ } ++ ++ // Place 4 bytes from the end ++ fseek(infile, -4, SEEK_END); ++ ++ b1=3D0; b2=3D0; b3=3D0; b4=3D0; ++ fread(&b4,1,1,infile); ++ fread(&b3,1,1,infile); ++ fread(&b2,1,1,infile); ++ fread(&b1,1,1,infile); ++ ++ val =3D 0; ++ temp =3D (long long int) b1; ++ temp <<=3D 24; ++ val =3D val | temp; ++ temp =3D (long long int) b2; ++ temp <<=3D 16; ++ val =3D val | temp; ++ temp =3D (long long int) b3; ++ temp <<=3D 8; ++ val =3D val | temp; ++ temp =3D (long long int) b4; ++ val =3D val | temp; ++ ++ //val =3D (b1 << 24) | (b2 << 16) + (b3 << 8) + b4; ++ ++ fclose(infile); ++ ++ if (prnlev>0) fprintf(stdout,"gzipFileSize: Uncompressed size of %s: = %lli\n",filename,val); ++ ++ return val; ++} ++ ++/*=20 ++ * bzip2FileSize() ++ * DRR: Return the uncompressed size of bzip2 file in bytes by counting= =20 ++ * all characters using bzcat and wc. ++ */ ++long long int bzip2FileSize(char *filename) { ++ long long int val; ++ char *command; ++ FILE *pipe; ++ ++ if (filename=3D=3DNULL) return -1; ++ // Use bzcat | wc -c to calc file size ++ command=3D(char*) malloc( (15 + strlen(filename)) * sizeof(char)); ++ sprintf(command,"bzcat %s | wc -c",filename); ++ if ((pipe=3Dpopen(command,"r"))=3D=3DNULL) { ++ fprintf(stdout,"Error: bzip2FileSize: Could not open %s for reading= .\n",filename); ++ fprintf(stdout," Check that bzcat and wc are present on your = system.\n"); ++ return -1; ++ } ++ fscanf(pipe,"%lli",&val); ++ pclose(pipe); ++ ++ if (prnlev>0) fprintf(stdout,"bzip2FileSize: Uncompressed size of %s:= %lli\n",filename,val); ++ ++ return val; ++} ++ ++/*=20 ++ * zipFileSize() ++ * DRR: Return the uncompressed size of zip file in bytes by counting=20 ++ * all characters using unzip and wc. ++ */ ++long long int zipFileSize(char *filename) { ++ long long int val; ++ char *command; ++ FILE *pipe; ++ ++ if (filename=3D=3DNULL) return -1; ++ // Use unzip -p | wc -c to calc file size ++ command=3D(char*) malloc( (18 + strlen(filename)) * sizeof(char)); ++ sprintf(command,"unzip -p %s | wc -c",filename); ++ if ((pipe=3Dpopen(command,"r"))=3D=3DNULL) { ++ fprintf(stdout,"Error: zipFileSize: Could not open %s for reading.\= n",filename); ++ fprintf(stdout," Check that unzip and wc are present on your = system.\n"); ++ return -1; ++ } ++ fscanf(pipe,"%lli",&val); ++ pclose(pipe); ++ ++ if (prnlev>0) fprintf(stdout,"zipFileSize: Uncompressed size of %s: %= lli\n",filename,val); ++ ++ return val; ++} ++ + /* DAN ROE: + * id_Filesig(): Attempt to identify the file type by first 3 hex vals. + * A filename or an open stream should be supplied. +@@ -689,7 +790,7 @@ + * -2: Internal error + */ + int id_Filesig(char *filename, FILE *infile) { +- int *h; ++ unsigned char *h; + int i, type; +=20 + /* Check that either filename or infile is specified, but not both */ +@@ -712,7 +813,7 @@ + rewind(infile); +=20 + /* Read first 3 bytes from file */ +- h=3D(int*) calloc(3,sizeof(int)); ++ h=3D(unsigned char*) calloc(3,sizeof(unsigned char)); + fread(h,1,1,infile); + fread(h+1,1,1,infile); + fread(h+2,1,1,infile); +diff -urN amber11.orig/AmberTools/src/ptraj/io.h amber11/AmberTools/src/= ptraj/io.h +--- amber11.orig/AmberTools/src/ptraj/io.h 2010-03-31 07:05:16.000000000= +0400 ++++ amber11/AmberTools/src/ptraj/io.h 2011-03-08 16:38:44.000000000 +030= 0 +@@ -76,6 +76,9 @@ +=20 + extern void doSystem(char *); + extern char * promptToOpenFile( FILE **, char *, char *, char *); ++extern long long int gzipFileSize(char *); ++extern long long int bzip2FileSize(char *); ++extern long long int zipFileSize(char *); + extern int id_Filesig(char *,FILE *); + extern int openFile( FILE **, char *, char *); + extern int promptUserResponse(FILE *, FILE *, char *, char *, int); +@@ -94,6 +97,9 @@ +=20 + extern void doSystem(); + extern char * promptToOpenFile(); ++extern long long int gzipFileSize(); ++extern long long int bzip2FileSize(); ++extern long long int zipFileSize(); + extern int id_Filesig(); + extern int openFile(); + extern int promptUserResponse(); +diff -urN amber11.orig/AmberTools/src/ptraj/ptraj.c amber11/AmberTools/s= rc/ptraj/ptraj.c +--- amber11.orig/AmberTools/src/ptraj/ptraj.c 2010-04-23 18:17:17.000000= 000 +0400 ++++ amber11/AmberTools/src/ptraj/ptraj.c 2011-03-08 16:38:44.000000000 += 0300 +@@ -2058,7 +2058,8 @@ + int lines_per_set; + int start =3D 1; + int stop =3D 1; +- int frame_lines, frame_size, title_size, seekable; ++ int frame_lines, title_size, seekable; ++ long long int file_size, frame_size; + long int endoffset; + float *binposScratch; + FILE *fp; +@@ -2414,12 +2415,34 @@ + fprintf(stderr, "WARNING in %s: Could not find file status for %s\n", = ROUTINE, filename); + return NULL; + } ++ ++ // Determine Uncompressed File Size for Nframes calculation ++ file_size=3D0; ++ if (trajInfo->compressType=3D=3D1) // Gzip ++ file_size=3DgzipFileSize(filename); ++ else if (trajInfo->compressType=3D=3D2) // Bzip2 ++ file_size=3Dbzip2FileSize(filename); ++ else if (trajInfo->compressType=3D=3D3) // Zip ++ file_size=3DzipFileSize(filename); ++ if (file_size<0) { ++ fprintf(stdout, ++ "ERROR in %s: Could not calculate uncompressed file siz= e for %s\n", ++ ROUTINE, filename); ++ return NULL; ++ } ++ if (file_size=3D=3D0) file_size=3Dframe_stat.st_size; ++ + if (prnlev>0) +- fprintf(stdout,"[%i] Title offset %u Frame Size %u File si= ze %lu\n", +- worldrank,trajInfo->titleSize,trajInfo->frameSize,frame= _stat.st_size); +- if (((frame_stat.st_size - trajInfo->titleSize) % (trajInfo->fram= eSize)) =3D=3D 0) { ++ fprintf(stdout,"[%i] Title offset %u Frame Size %u File si= ze %lli\n", ++ worldrank,trajInfo->titleSize,trajInfo->frameSize,file_= size); ++ frame_size =3D (long long int) trajInfo->titleSize; ++ file_size =3D file_size - frame_size; // Subtract title size from= file total size. ++ frame_size =3D (long long int) trajInfo->frameSize; ++ trajInfo->Nframes =3D (int) (file_size / frame_size); ++ if (prnlev>0) fprintf(stdout," File has %i frames.\n",trajInfo= ->Nframes); ++ if ( (file_size % frame_size) =3D=3D 0 ) { + seekable =3D 1; +- stop =3D (int) ((frame_stat.st_size - trajInfo->titleSize) / trajInfo-= >frameSize); ++ stop =3D trajInfo->Nframes; + } else { + stop =3D -1; + seekable =3D 0; +@@ -2538,7 +2561,8 @@ + printfone(" With this version of the code, this will likely lead t= o program failure!!!\n"); + } +=20 +- ++ // Set number of frames. Amber trajectory sets Nframes above ++ if (trajInfo->Nframes=3D=3D0 && stop>0) trajInfo->Nframes=3Dstop; + trajInfo->start =3D start; + trajInfo->stop =3D stop; + trajInfo->offset =3D 1; +@@ -4182,7 +4206,7 @@ + fprintf(stderr,"Could not get replica temperature from fi= le# %i\n",i); + break; + } +- fprintf(stdout," Replica %i mytemp=3D%lf ",i,repTemp); /= /DEBUG=20 ++ if (prnlev>0) fprintf(stdout," Replica %i mytemp=3D%lf ",= i,repTemp); //DEBUG=20 + if (repTemp=3D=3DcurrentCoordinateInfo->remdtrajtemp) { + if (prnlev>0) fprintf(stdout, + " REMD target temperature (%lf) found (%lf) at rep= lica index %i\n", +@@ -7078,6 +7102,7 @@ + stackType *sp, *argumentStack; + ptrajState *startingState, *currentState, **statep; + char *continuation; ++ int totalFrames; +=20 + int readCoordinates; + int processCoordinates; +@@ -7140,8 +7165,8 @@ + */ +=20 + argumentStack =3D NULL; +- while ( (bufferp =3D fgets(buffer, BUFFER_SIZE, infile)) !=3D NULL && +- strcmp(bufferp, "go\n") !=3D 0 ) { ++ while ( (bufferp =3D fgets(buffer, BUFFER_SIZE, infile)) !=3D NULL ) = { ++ if ( strncmp(bufferp, "go", 2) =3D=3D 0 ) break; +=20 + continuation =3D bufferp; + while ( continuation !=3D NULL ) { +@@ -7218,18 +7243,25 @@ + */ +=20 + startingState->maxFrames =3D 0; ++ totalFrames=3D0; + for (sp =3D transformFileStack; sp !=3D NULL; sp =3D sp->next) { + currentCoordinateInfo =3D (coordinateInfo *) sp->entry; +=20 ++ fprintf(stdout," %s: %i frames.\n",currentCoordinateInfo->filename= ,currentCoordinateInfo->Nframes); ++ + startingState->maxFrames +=3D (currentCoordinateInfo->stop -=20 + currentCoordinateInfo->start) / + currentCoordinateInfo->offset + 1; ++ // In case we dont know how many frames will be processed, use tota= l number of frames ++ totalFrames +=3D currentCoordinateInfo->Nframes; + } +=20 + printfone("\nPTRAJ: Successfully read the input file.\n"); +- if (startingState->maxFrames =3D=3D -1) ++ if (startingState->maxFrames =3D=3D -1) { + printfone(" Coordinate processing will occur until EOF (unkno= wn number of frames).\n"); +- else ++ // Use total frames for action memory alloc. ++ startingState->maxFrames =3D totalFrames; ++ } else + printfone(" Coordinate processing will occur on %i frames.\n"= ,=20 + startingState->maxFrames); + printfone(" Summary of I/O and actions follows:\n\n"); +diff -urN amber11.orig/AmberTools/src/ptraj/trajectory.c amber11/AmberTo= ols/src/ptraj/trajectory.c +--- amber11.orig/AmberTools/src/ptraj/trajectory.c 2010-03-31 07:05:16.0= 00000000 +0400 ++++ amber11/AmberTools/src/ptraj/trajectory.c 2011-03-08 16:38:44.000000= 000 +0300 +@@ -2341,15 +2341,22 @@ +=20 + /* trajFile_fseek() + * Wrapper for fseek. Seek to a given frame.=20 ++ * fseeko is used for better compatibility with large files. To avoid ++ * losing bits each variable is explicitly converted to off_t in offset= =20 ++ * calculation. + */ + int trajFile_fseek(coordinateInfo *C, int frame) { + int err; ++ off_t offset; +=20 + if (C=3D=3DNULL) return -1; +=20 +- if (C->isMPI=3D=3D0)=20 +- err=3Dfseek(C->file, C->titleSize+(frame*C->frameSize), SEEK_SET); +- else ++ if (C->isMPI=3D=3D0) { ++ offset =3D (off_t) frame; ++ offset *=3D (off_t) C->frameSize; ++ offset +=3D (off_t) C->titleSize; ++ err=3Dfseeko(C->file, offset, SEEK_SET); ++ } else + err=3Dparallel_fseek(C,frame); +=20 + return err; +diff -urN amber11.orig/AmberTools/src/ptraj/trajectory.h amber11/AmberTo= ols/src/ptraj/trajectory.h +--- amber11.orig/AmberTools/src/ptraj/trajectory.h 2010-03-31 07:05:16.0= 00000000 +0400 ++++ amber11/AmberTools/src/ptraj/trajectory.h 2011-03-08 16:38:44.000000= 000 +0300 +@@ -168,6 +168,7 @@ + char *filename; // File name + int start; // Frame to start processing + int stop; // Frame to end processing ++ int Nframes; // Total number of frames in the file. + int offset; // # of frames to skip + int append; // File will be appended to + int isBox; // File has box information +@@ -230,6 +231,7 @@ + _p_->filename =3D NULL; \ + _p_->start =3D 1; \ + _p_->stop =3D -1; \ ++ _p_->Nframes =3D 0; \ + _p_->offset =3D 1; \ + _p_->append =3D 0; \ + _p_->isBox =3D 0; \ +diff -urN amber11.orig/AmberTools/src/rism/amber_rism_interface.f amber1= 1/AmberTools/src/rism/amber_rism_interface.f +--- amber11.orig/AmberTools/src/rism/amber_rism_interface.f 2010-04-07 1= 6:55:55.000000000 +0400 ++++ amber11/AmberTools/src/rism/amber_rism_interface.f 2011-03-08 16:38:= 44.000000000 +0300 +@@ -501,7 +501,8 @@ + call timer_stop(TIME_REORIENT) + !linproj predict + call timer_start(TIME_CRDINTERP) +- call fce_force(fce_o,ff,rism_3d%solu%ratu) ++ if(rismprm%apply_rism_force=3D=3D1)& ++ call fce_force(fce_o,ff,rism_3d%solu%ratu) + call timer_stop(TIME_CRDINTERP) +=20 + call timer_start(TIME_REORIENT) +@@ -537,16 +538,17 @@ + end if + #else /*SANDER*/ + #endif /*SANDER*/ +- call rism3d_force(rism_3d,ff) +- if(rismprm%zerofrc=3D=3D1)then ++ if(rismprm%apply_rism_force=3D=3D1)then ++ call rism3d_force(rism_3d,ff) ++ if(rismprm%zerofrc=3D=3D1)then + #ifdef MPI +- call corr_drift(ff,rism_3d%solu%mass,rism_3d%solu%natom,& +- mpirank,mpisize,mpicomm) ++ call corr_drift(ff,rism_3d%solu%mass,rism_3d%solu%natom,& ++ mpirank,mpisize,mpicomm) + #else +- call corr_drift(ff,rism_3d%solu%mass,rism_3d%solu%natom) ++ call corr_drift(ff,rism_3d%solu%mass,rism_3d%solu%natom) + #endif /*MPI*/ ++ end if + end if +- + !get the excess chemical potential + call timer_start(TIME_EXCHEM) + if(rismprm%gauss_fluct =3D=3D 0)then +@@ -563,12 +565,12 @@ + #endif /*defined(MPI)*/ + end if + call timer_stop(TIME_EXCHEM) +- ++ =20 + #ifdef RISM_CRDINTERP + call timer_start(TIME_REORIENT) + call orient(rism_3d,ff,qback) + call timer_stop(TIME_REORIENT) +- if(rismprm%fcestride >0)then ++ if(rismprm%fcestride >0 .and. rismprm%apply_rism_force=3D=3D1)then + call timer_start(TIME_SAVECRDINTERP) + call fce_update(fce_o,ff,rism_3d%solu%ratu) + call timer_stop(TIME_SAVECRDINTERP) +@@ -586,7 +588,6 @@ +=20 + end if + if(rismprm%apply_rism_force=3D=3D1) frc =3D frc+ff +- call flush(6) + return + end subroutine rism_force +=20 +@@ -1087,6 +1088,7 @@ + subroutine rism_writeSolvDistF(this,step) + use amber_rism_interface + use rism3d_opendx ++ use safemem + implicit none + #if defined(MPI) + include 'mpif.h' +@@ -1097,9 +1099,18 @@ + character(len=3D16) :: cstep + character(len=3D64) :: suffix + integer :: unit =3D 99,iostat=3D0 ++#ifdef MPI ++ integer :: err ++ _REAL_, pointer::work(:,:,:)=3D>NULL() ++#endif /*MPI*/ =20 + #ifdef RISM_DEBUG + write(6,*) "printrism" + #endif ++#ifdef MPI ++ if(len_trim(guvfile) /=3D 0 .or. len_trim(huvfile) /=3D 0)then ++ work =3D> reallocate_pointer(work, this%ng3(1), this%ng3(2), this%= nz_local) ++ end if ++#endif /*MPI*/ + !................... outputting Guv and Cuv profiles ................= ... + do iv=3D1,this%solv%natom + write(cstep,'(i16)') step +@@ -1112,9 +1123,15 @@ + call mexit(6,1) + end if + # if defined(MPI) ++ do k=3D1,this%nz_local ++ do j=3D1,this%ng3(2) ++ do i=3D1,this%ng3(1) ++ work(i,j,k) =3D this%guv(i+(j-1)*(this%ng3(1)+2)+(k-1)= *(this%ng3(1)+2)*this%ng3(2),iv) ++ end do ++ end do ++ end do + call writeDX(unit,& +- (/(((this%guv(i+(j-1)*(this%ng3(1)+2)+(k-1)*(this%ng3(1)+2= )*this%ng3(2),iv)& +- ,i=3D1,this%ng3(1)),j=3D1,this%ng3(2)),k=3D1,this%nz_local= )/),& ++ work,& + this%boxlen,this%ng3_local,this%ng3(3),this%ratucm,& + mpirank,mpisize,mpicomm) + # else +@@ -1131,9 +1148,16 @@ + call mexit(6,1) + end if + # if defined(MPI) ++ =20 ++ do k=3D1,this%nz_local ++ do j=3D1,this%ng3(2) ++ do i=3D1,this%ng3(1) ++ work(i,j,k) =3Dthis%huv(i+(j-1)*(this%ng3(1)+2)+(k-1)*= (this%ng3(1)+2)*this%ng3(2),iv) ++ end do ++ end do ++ end do + call writeDX(unit,& +- (/(((this%huv(i+(j-1)*(this%ng3(1)+2)+(k-1)*(this%ng3(1)+2= )*this%ng3(2),iv)& +- ,i=3D1,this%ng3(1)),j=3D1,this%ng3(2)),k=3D1,this%nz_local= )/),& ++ work,& + this%boxlen,this%ng3_local,this%ng3(3),this%ratucm,& + mpirank,mpisize,mpicomm) + # else +@@ -1160,6 +1184,9 @@ + if(mpirank=3D=3D0)close(unit) + endif + end do ++#ifdef MPI ++ err =3D safe_deallocate(work) ++#endif /*MPI*/ + end subroutine rism_writeSolvDistF +=20 + !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!= !!!!!!!!!!! +diff -urN amber11.orig/AmberTools/src/rism/rism3d_c.f amber11/AmberTools= /src/rism/rism3d_c.f +--- amber11.orig/AmberTools/src/rism/rism3d_c.f 2010-04-07 16:55:55.0000= 00000 +0400 ++++ amber11/AmberTools/src/rism/rism3d_c.f 2011-03-08 16:38:44.000000000= +0300 +@@ -911,7 +911,7 @@ + !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!= !!!!!!!!! + subroutine rism3d_aexchem_sp (this,xmu0,xmu0sp,egf) + use constants, only : PI,KB,AMBER_ELECTROSTATIC2 +- use rism_util, only : gaussquad_legendre ++ use rism_util, only : gaussquad_legendre, checksum + implicit none + #if defined(MPI) + include 'mpif.h' +@@ -947,132 +947,130 @@ + call flush(6) + #endif /*RISM_DEBUG*/ +=20 ++ !.....total charge of solute ++ qut =3D sum(this%solu%charge) + !.....getting the numerical long-range contribution + egf =3D 0 +- eqkt =3D AMBER_ELECTROSTATIC2/KB/this%solv%temperature +- +- Nintmx =3D 200 +- if(Nintmx > ntvlmx)then +- write(6,'(1X,"Nintmx gt ntvlmx",I10)')ntvlmx +- call mexit(6,1) +- endif +- +- !.....initialize gauss-legendre integration +- call gaussquad_legendre (0d0,1d0,argum,weight,Nintmx) +- sumhc =3D 0.d0 +- sumh2 =3D 0.d0 +- +- !.....k loop +- do ik =3D 1, Nintmx +- +- k =3D argum(ik)/(1.d0-argum(ik)) +- +- !.....Bessel part +- sumb =3D 0.d0 +- +- do i=3D2,this%solu%natom +- do j=3D1,i-1 +- +- !......... site separation .......... +- dx =3D this%solu%ratu(1,i) - this%solu%ratu(1,j) +- dy =3D this%solu%ratu(2,i) - this%solu%ratu(2,j) +- dz =3D this%solu%ratu(3,i) - this%solu%ratu(3,j) +- +- r2 =3D dx*dx + dy*dy + dz*dz +- +- xarg =3D this%solv%xappa*k*sqrt(r2) +- if(xarg =3D=3D 0.d0) & +- sumb =3D sumb + 1.d0*this%solu%charge(i)*this%solu%= charge(j) +- if(xarg /=3D 0.d0) & +- sumb =3D sumb + sin(xarg)/xarg *this%solu%charge(i)= *this%solu%charge(j) +=20 ++ if(this%mpirank=3D=3D0)then =20 ++ eqkt =3D AMBER_ELECTROSTATIC2/KB/this%solv%temperature ++ Nintmx =3D 200 ++ if(Nintmx > ntvlmx)then ++ write(6,'(1X,"Nintmx gt ntvlmx",I10)')ntvlmx ++ call mexit(6,1) ++ endif ++ =20 ++ !.....initialize gauss-legendre integration ++ call gaussquad_legendre (0d0,1d0,argum,weight,Nintmx) ++ sumhc =3D 0.d0 ++ sumh2 =3D 0.d0 ++ =20 ++ !.....k loop ++ do ik =3D 1, Nintmx ++ =20 ++ k =3D argum(ik)/(1.d0-argum(ik)) ++ =20 ++ !.....Bessel part ++ sumb =3D 0.d0 ++ =20 ++ do i=3D2,this%solu%natom ++ do j=3D1,i-1 ++ =20 ++ !......... site separation .......... ++ dx =3D this%solu%ratu(1,i) - this%solu%ratu(1,j) ++ dy =3D this%solu%ratu(2,i) - this%solu%ratu(2,j) ++ dz =3D this%solu%ratu(3,i) - this%solu%ratu(3,j) ++ =20 ++ r2 =3D dx*dx + dy*dy + dz*dz ++ =20 ++ xarg =3D this%solv%xappa*k*sqrt(r2) ++ if(xarg =3D=3D 0.d0) & ++ sumb =3D sumb + 1.d0*this%solu%charge(i)*this%so= lu%charge(j) ++ if(xarg /=3D 0.d0) & ++ sumb =3D sumb + sin(xarg)/xarg *this%solu%charge= (i)*this%solu%charge(j) ++ =20 ++ enddo + enddo +- enddo +- +- sumb =3D sumb*2.d0 +- +- do i=3D1,this%solu%natom +- sumb =3D sumb + 1.d0*this%solu%charge(i)*this%solu%charge(i= ) +- enddo +- +- !.....end of Bessel part +- +- x2arg =3D (k*this%solv%xappa*this%solv%smear)**2 +- k2 =3D k**2 +- +- denom =3D argum(ik)**2+(1.0d0-argum(ik))**2 +- +- sumhc =3D sumhc + & +- exp(-x2arg/2.d0)/denom*sumb*weight(ik) +- sumh2 =3D sumh2 + & +- exp(-x2arg/2.d0)*argum(ik)**2/(denom**2)*sumb*weight(ik) +- +- enddo +- +- !.....end of k-loop +- +- !.....total charge of solute +- qut =3D 0.d0 +- do i =3D 1,this%solu%natom +- qut =3D qut + this%solu%charge(i) +- enddo +- !.....site xappa +- if (this%closure =3D=3D KH) then ++ =20 ++ sumb =3D sumb*2.d0 ++ =20 ++ do i=3D1,this%solu%natom ++ sumb =3D sumb + 1.d0*this%solu%charge(i)*this%solu%charg= e(i) ++ enddo ++ =20 ++ !.....end of Bessel part ++ =20 ++ x2arg =3D (k*this%solv%xappa*this%solv%smear)**2 ++ k2 =3D k**2 ++ =20 ++ denom =3D argum(ik)**2+(1.0d0-argum(ik))**2 ++ =20 ++ sumhc =3D sumhc + & ++ exp(-x2arg/2.d0)/denom*sumb*weight(ik) ++ sumh2 =3D sumh2 + & ++ exp(-x2arg/2.d0)*argum(ik)**2/(denom**2)*sumb*weight(i= k) ++ =20 ++ enddo ++ =20 ++ !.....end of k-loop ++ =20 ++ !.....site xappa ++ if (this%closure =3D=3D KH) then ++ do iv =3D 1,this%solv%natom ++ if(qut*this%solv%charge_sp(iv) <=3D 0.d0) & ++ xmuh2lr(iv) =3D 4.d0*PI/(this%solv%dielconst) * thi= s%solv%rho(iv)*this%solv%charge_sp(iv)**2 ++ if(qut*this%solv%charge_sp(iv) > 0.d0) & ++ xmuh2lr(iv) =3D 0.d0 ++ xmuhclr(iv) =3D 4.d0*PI/(this%solv%dielconst) * this%sol= v%rho(iv)*this%solv%charge(iv)*this%solv%charge_sp(iv) ++ enddo ++ else ++ do iv =3D 1,this%solv%natom ++ xmuh2lr(iv) =3D 4.d0*PI/(this%solv%dielconst) * this%sol= v%rho(iv)*this%solv%charge_sp(iv)**2 ++ xmuhclr(iv) =3D 4.d0*PI/(this%solv%dielconst) * this%sol= v%rho(iv)*this%solv%charge(iv)*this%solv%charge_sp(iv) ++ enddo ++ endif ++ =20 ++ !.....unit for xappa + do iv =3D 1,this%solv%natom +- if(qut*this%solv%charge_sp(iv) <=3D 0.d0) & +- xmuh2lr(iv) =3D 4.d0*PI/(this%solv%dielconst) * this%s= olv%rho(iv)*this%solv%charge_sp(iv)**2 +- if(qut*this%solv%charge_sp(iv) > 0.d0) & +- xmuh2lr(iv) =3D 0.d0 +- xmuhclr(iv) =3D 4.d0*PI/(this%solv%dielconst) * this%solv%r= ho(iv)*this%solv%charge(iv)*this%solv%charge_sp(iv) ++ xmuh2lr(iv) =3D xmuh2lr(iv) * eqkt ++ xmuhclr(iv) =3D xmuhclr(iv) * eqkt + enddo +- else ++ =20 ++ !.....divided by total xappa ++ if(this%solv%xappa /=3D 0.d0)then ++ do iv =3D 1,this%solv%natom ++ xmuh2lr(iv) =3D xmuh2lr(iv) / this%solv%xappa ++ xmuhclr(iv) =3D xmuhclr(iv) / this%solv%xappa ++ enddo ++ else ++ do iv =3D 1,this%solv%natom ++ xmuh2lr(iv) =3D 0.d0 ++ xmuhclr(iv) =3D 0.d0 ++ enddo ++ endif ++ =20 ++ !.....multiplying xmulr by integral + do iv =3D 1,this%solv%natom +- xmuh2lr(iv) =3D 4.d0*PI/(this%solv%dielconst) * this%solv%r= ho(iv)*this%solv%charge_sp(iv)**2 +- xmuhclr(iv) =3D 4.d0*PI/(this%solv%dielconst) * this%solv%r= ho(iv)*this%solv%charge(iv)*this%solv%charge_sp(iv) ++ xmuh2lr(iv) =3D xmuh2lr(iv)*sumh2 ++ xmuhclr(iv) =3D - xmuhclr(iv)*sumhc + enddo +- endif +- +- !.....unit for xappa +- do iv =3D 1,this%solv%natom +- xmuh2lr(iv) =3D xmuh2lr(iv) * eqkt +- xmuhclr(iv) =3D xmuhclr(iv) * eqkt +- enddo +- +- !.....divided by total xappa +- if(this%solv%xappa /=3D 0.d0)then ++ =20 ++ sumh2 =3D 0.d0 ++ sumhc =3D 0.d0 + do iv =3D 1,this%solv%natom +- xmuh2lr(iv) =3D xmuh2lr(iv) / this%solv%xappa +- xmuhclr(iv) =3D xmuhclr(iv) / this%solv%xappa ++ sumh2 =3D sumh2 + xmuh2lr(iv) ++ sumhc =3D sumhc + xmuhclr(iv) + enddo +- else ++ =20 ++ !.....J devided by KT ++ sumh2 =3D sumh2 / (PI*this%solv%dielconst) * eqkt ++ sumhc =3D sumhc / PI * eqkt + do iv =3D 1,this%solv%natom +- xmuh2lr(iv) =3D 0.d0 +- xmuhclr(iv) =3D 0.d0 ++ xmuh2lr(iv) =3D xmuh2lr(iv) / (PI*this%solv%dielconst) * eq= kt ++ xmuhclr(iv) =3D xmuhclr(iv) / PI * eqkt + enddo +- endif +- +- !.....multiplying xmulr by integral +- do iv =3D 1,this%solv%natom +- xmuh2lr(iv) =3D xmuh2lr(iv)*sumh2 +- xmuhclr(iv) =3D - xmuhclr(iv)*sumhc +- enddo +- +- sumh2 =3D 0.d0 +- sumhc =3D 0.d0 +- do iv =3D 1,this%solv%natom +- sumh2 =3D sumh2 + xmuh2lr(iv) +- sumhc =3D sumhc + xmuhclr(iv) +- enddo +- +- !.....J devided by KT +- sumh2 =3D sumh2 / (PI*this%solv%dielconst) * eqkt +- sumhc =3D sumhc / PI * eqkt +- do iv =3D 1,this%solv%natom +- xmuh2lr(iv) =3D xmuh2lr(iv) / (PI*this%solv%dielconst) * eqkt +- xmuhclr(iv) =3D xmuhclr(iv) / PI * eqkt +- enddo +- xmulr =3D sumh2 + sumhc +- ++ xmulr =3D sumh2 + sumhc ++ end if + !.................. calculating xMu0 by PLHNC closure ...........= ....... + if (this%closure =3D=3D KH) then + dxmu =3D 0.d0 +@@ -1232,13 +1230,20 @@ + xmu0sp(iv) =3D xmu0sp(iv) * (this%boxvol/this%ngr) + enddo +=20 +- !.....add long-range part +- xmu0 =3D xmu0 + (xmulr) +- egf =3D egf + (xmulr) +- do iv=3D1,this%solv%natom +- xmu0sp(iv) =3D xmu0sp(iv) + xmuh2lr(iv) + xmuhclr(iv) +- enddo +- ++ !.....add long-range part but only on the master process so we do= n't over count ++ !.....this contribution. ++!!$ write(0,*) "pre lr", this%mpirank, xmu0 ++!!$ write(0,*) checksum(this%huv,product(shape(this%huv)),this%mpi= comm), & ++!!$ checksum(this%cuv,product(shape(this%cuv)),this%mpicomm),= & ++!!$ checksum(this%uuv,product(shape(this%uuv)),this%mpicomm) ++ if(this%mpirank=3D=3D0)then ++ xmu0 =3D xmu0 + (xmulr) ++ egf =3D egf + (xmulr) ++ do iv=3D1,this%solv%natom ++ xmu0sp(iv) =3D xmu0sp(iv) + xmuh2lr(iv) + xmuhclr(iv) ++ enddo ++ end if ++!!$ write(0,*) "post lr", this%mpirank, xmu0 + return + end subroutine rism3d_aexchem_sp +=20 +@@ -2322,6 +2327,7 @@ + subroutine asympch(this,huvk0) + use constants, only : PI, FOURPI,& + AMBER_ELECTROSTATIC2,KB ++ use rism_util, only : checksum + implicit none + #if defined(MPI) + include 'mpif.h' +@@ -2339,9 +2345,7 @@ + _REAL_ :: xappa2,smear2_4 + _REAL_ :: asymhr_coeff + _REAL_,save :: asymhr_coeff_at_cut=3D0,asymcr_coeff_at_cut=3D0 +- _REAL_,save :: erfcAtCut=3D0,erfcAtNegCut=3D0,cut=3D15.5d0 +-!! _REAL_,save :: erfcAtCut=3D0,erfcAtNegCut=3D0,cut=3D999d0 +-! !linear spacing of the grid ++ _REAL_,save :: erfcAtCut=3D0,erfcAtNegCut=3D0,cut=3D4d0,maxcut + !offset :: z-axis offset (important for spatially distributed MPI= ) + _REAL_ :: offset + ! !number of gridpoints in each direction to use +@@ -2351,7 +2355,7 @@ + _REAL_ :: erfc + external erfc + integer :: irank,ierr,i +- _REAL_:: checksum,mpitmp ++ _REAL_:: mpitmp +=20 + half_smear_root_pi=3Dsqrt(PI)*this%solv%smear/2d0 + half_xappa_smear=3Dthis%solv%xappa*this%solv%smear/2d0 +@@ -2361,7 +2365,9 @@ + asymhr_coeff=3Dexp(-(this%solv%xappa**2)*(this%solv%smear**2)/4d0= )* & + (2d0*exp(-(this%solv%smear*this%solv%xappa/2d0)**2)/(sqrt(PI= )*this%solv%smear) & + - this%solv%xappa * erfc(this%solv%xappa*this%solv%smear/2d0= )) +- do while(exp(-quarter_xappa2_smear2)-asymhr_coeff_at_cut > 1d-7 .= and. 1d0-asymcr_coeff_at_cut > 1d-7) ++ maxcut =3D sqrt(sum(this%boxlen**2)) ++ do while((exp(-quarter_xappa2_smear2)-asymhr_coeff_at_cut > 1d-7 = .or. 1d0-asymcr_coeff_at_cut > 1d-7)& ++ .and. cut < maxcut) + erfcAtCut =3D erfc(cut) + erfcAtNegCut =3D erfc(-cut) + asymhr_coeff_at_cut=3Dexp(-quarter_xappa2_smear2) & +@@ -2370,10 +2376,10 @@ + !(erfcAtNegCut - erfcAtCut)/2d0 + asymcr_coeff_at_cut=3D(1d0-erfc(cut/this%solv%smear)) + cut =3D cut+.1d0 +- ! write(6,*)'cut coeff',asymhr_coeff_at_cut,asymcr_coeff_= at_cut ++! write(0,*)'cut coeff',this%mpirank,asymhr_coeff_at_cut,asymcr= _coeff_at_cut + end do + #ifdef RISM_DEBUG +- write(6,*)'cut coeff',cut,asymhr_coeff_at_cut,asymcr_coeff_at_cut ++ write(0,*)'cut coeff',cut,exp(-quarter_xappa2_smear2)-asymhr_coef= f_at_cut,asymcr_coeff_at_cut + #endif /*RISM_DEBUG*/ + !.....initialize + this%asymcr=3D0d0 +@@ -2569,7 +2575,7 @@ + this%asymcr =3D this%asymcr * factor + this%asymhr =3D this%asymhr * factor + this%asymck =3D this%asymck * (factor / this%boxvol) +- this%asymhk =3D this%asymhk * (factor / this%boxvol)/2d0/PI**2 ++ this%asymhk =3D this%asymhk * (factor / this%boxvol) +=20 + !?WHY IS THIS ONLY FOR ny_start=3D=3D0?! + if(this%ny_start=3D=3D0)then +@@ -2591,35 +2597,22 @@ + end if + #ifdef RISM_DEBUG + # ifdef MPI =20 +- checksum =3D sum(this%asymck) +-# ifdef USE_MPI_IN_PLACE +- call mpi_allreduce(MPI_IN_PLACE,checksum,1,MPI_DOUBLE_PRECISION,mpi= _sum,this%mpicomm,ierr) +-# else +- call mpi_allreduce(checksum,mpitmp,1,MPI_DOUBLE_PRECISION,mpi_sum,t= his%mpicomm,ierr) +- checksum =3D mpitmp +-# endif /*USE_MPI_IN_PLACE*/ +- if(this%mpirank =3D=3D 0)then +- write(6,*) "SUM this%asymck", this%mpirank, checksum ++ write(6,*) "SUM this%asymhr", this%mpirank, & ++ checksum(this%asymhr,product(shape(this%asymhr)), this%mpic= omm), sum(this%asymhr) ++ write(6,*) "SUM this%asymcr", this%mpirank, & ++ checksum(this%asymcr,product(shape(this%asymcr)), this%mpic= omm), sum(this%asymcr) + call flush(6) +- end if +- checksum =3D sum(this%asymhk) +-# ifdef USE_MPI_IN_PLACE +- call mpi_allreduce(MPI_IN_PLACE,checksum,1,MPI_DOUBLE_PRECISION,mpi= _sum,this%mpicomm,ierr) +-# else +- call mpi_allreduce(checksum,mpitmp,1,MPI_DOUBLE_PRECISION,mpi_sum,t= his%mpicomm,ierr) +- checksum =3D mpitmp +-# endif /*USE_MPI_IN_PLACE*/ +- if(this%mpirank =3D=3D 0)then +- write(6,*) "SUM this%asymhk", this%mpirank, checksum +- call flush(6) +- end if + # else +- write(6,*)"SUM this%asymcr ",size(this%asymcr),sum(this%asymcr= ),& +- sum(this%asymcr(1:this%ngr_local/2)),sum(this%asymcr(this= %ngr_local/2+1:this%ngr_local)) +- write(6,*)"SUM this%asymhr ",size(this%asymhr),sum(this%asymhr= ),& +- sum(this%asymhr(1:this%ngr_local/2)),sum(this%asymhr(this= %ngr_local/2+1:this%ngr_local)) ++ write(6,*) cut, asymhr_coeff_at_cut, asymcr_coeff_at_cut ++ write(6,*)"SUM this%asymcr ",size(this%asymcr),sum(this%asymcr),& ++ sum(this%asymcr(1:this%ngr_local/2)),sum(this%asymcr(this%ngr_= local/2+1:this%ngr_local)) ++ write(6,*)"SUM this%asymhr ",size(this%asymhr),sum(this%asymhr),& ++ sum(this%asymhr(1:this%ngr_local/2)),sum(this%asymhr(this%ngr_= local/2+1:this%ngr_local)) ++ stop ++# endif /*MPI */ + #endif /*RISM_DEBUG*/ + #ifdef RISM_DEBUG ++# ifdef MPI =20 + write(6,*) "RANK",this%mpirank,factor,this%boxvol + write(6,'(a,i4,f15.10,f15.10)') "SUM this%asymck",this%ngk,sum(th= is%asymck),sum(this%asymck(3:)) + write(6,'(a,i4,f15.10,f15.10)') "SUM this%asymhk",this%ngk,sum(th= is%asymhk),sum(this%asymhk(3:)) +diff -urN amber11.orig/AmberTools/src/rism/rism3d_opendx.f amber11/Amber= Tools/src/rism/rism3d_opendx.f +--- amber11.orig/AmberTools/src/rism/rism3d_opendx.f 2010-04-07 16:55:55= .000000000 +0400 ++++ amber11/AmberTools/src/rism/rism3d_opendx.f 2011-03-08 16:38:44.0000= 00000 +0300 +@@ -55,28 +55,37 @@ + contains + subroutine writeDX (unit, data, rism_box, n,nz_total,ratucm & + #ifdef MPI +- ,rank,size,comm & ++ ,rank,nproc,comm & + #endif /*MPI*/ + )=20 ++ use safemem + implicit none + #if defined(MPI) + include 'mpif.h' +- integer, intent(in) :: rank,size,comm ++ integer, intent(in) :: rank,nproc,comm + #else +- integer,parameter :: rank =3D 0, size=3D1 ++ integer,parameter :: rank =3D 0, nproc=3D1 + #endif /*defined(MPI)*/ + integer, intent(in) :: nz_total + integer,intent(in) :: unit, n(3) + _REAL_,intent(in) :: data(n(1),n(2),n(3)), rism_box(3),ratucm(3) + integer :: i,j,k, irank, ierr,count,icount +- integer :: nz_offset(size),nz_local(size) ++ integer :: nz_offset(nproc),nz_local(nproc) + integer, parameter :: dataperline=3D3 +- _REAL_ :: z_data(nz_total) ++#ifdef MPI ++ integer :: err ++ _REAL_,pointer :: z_data(:)=3D>NULL() ++#endif /*MPI*/ + #ifdef RISM_DEBUG ++ + write(6,*) "writeDX",rism_box,ratucm + call flush(6) + #endif /*RISM_DEBUG*/ +- ++!!$ do i =3D 1,nproc ++!!$ if(rank=3D=3Di)& ++!!$ write(0,*) "DX",rank,sum(data)/(rank+1),n(3) ++!!$ call mpi_barrier(comm,ierr) ++!!$ end do + if(rank=3D=3D0)then + write(unit,"(a,i8,i8,i8)") "object 1 class gridpositions counts"= ,n(1),n(2),nz_total + write(unit,"(a,3(f15.8))") "origin ",ratucm(1)-rism_box(1)/2,rat= ucm(2)-rism_box(2)/2,ratucm(3)-rism_box(3)/2 +@@ -89,9 +98,14 @@ + end if + count =3D 0 + #if defined(MPI) ++ z_data =3D>reallocate_pointer(z_data,nz_total) + call mpi_gather(n(3),1,mpi_integer,nz_local,1,mpi_integer,0,comm,ie= rr) + nz_offset(1) =3D 0 +- nz_offset(2:) =3D nz_local(1:size-1) ++ do i =3D 2, nproc ++ nz_offset(i) =3Dsum( nz_local(1:i-1)) ++ end do ++!!$ if(rank=3D=3D0)& ++!!$ write(0,*) "NZ",rank,nz_offset, nz_local + #endif /*defined(MPI)*/ + do i=3D1,n(1) + do j=3D1,n(2) +@@ -122,5 +136,8 @@ + end if + write(unit,"(a)") 'object "Untitled" call field' + end if ++#ifdef MPI ++ err =3D safe_deallocate(z_data) ++#endif /*MPI*/ + end subroutine writeDX + end module rism3d_opendx +diff -urN amber11.orig/AmberTools/src/rism/rism_fft.f amber11/AmberTools= /src/rism/rism_fft.f +--- amber11.orig/AmberTools/src/rism/rism_fft.f 2010-04-07 16:55:55.0000= 00000 +0400 ++++ amber11/AmberTools/src/rism/rism_fft.f 2011-03-08 16:38:44.000000000= +0300 +@@ -205,19 +205,23 @@ + ! Normalizing while Forward FFT (KEY=3D1) * + !******************************************************************= ***** + subroutine rlft3i (data, ng3, key,n_local,plan) ++ use safemem + implicit none + integer :: ng3(3), key + integer :: n_local + integer*8,intent(in) :: plan +- _REAL_ :: data((ng3(1)+2)*ng3(2)*n_local) +- _REAL_ :: work((ng3(1)+2)*ng3(2)*n_local) ++! _REAL_ :: data((ng3(1)+2)*ng3(2)*n_local) ++! _REAL_ :: work((ng3(1)+2)*ng3(2)*n_local) ++ _REAL_ :: data(:) ++ _REAL_,pointer :: work(:) + integer :: ngr, ngr_local,ngk_local, ig, ierr + integer, parameter :: FFTW_TRANSPOSED_ORDER=3D1, FFTW_NORMAL_ORDE= R=3D0 + !....................... R-space data array size ................= ....... + # ifdef RISM_DEBUG +- write(6,*) "rlft3i",n_local +- call flush(6) ++ write(0,*) "rlft3i",n_local ++ call flush(0) + # endif /*RISM_DEBUG*/ ++ work=3D>reallocate_pointer(work,size(data)) + ngr =3D ng3(1)*ng3(2)*ng3(3) + ngr_local =3D ng3(1)*ng3(2)*n_local + ngk_local =3D (ng3(1)+2)*ng3(2)*n_local +@@ -230,6 +234,7 @@ + call rfftwnd_f77_mpi( plan,1,data,work,1, & + FFTW_TRANSPOSED_ORDER) + end if ++ ierr =3D safe_deallocate(work) + end subroutine rlft3i +=20 + #else /*defined(MPI)*/ +diff -urN amber11.orig/AmberTools/src/sff/mm_options.l amber11/AmberTool= s/src/sff/mm_options.l +--- amber11.orig/AmberTools/src/sff/mm_options.l 2010-03-31 07:05:17.000= 000000 +0400 ++++ amber11/AmberTools/src/sff/mm_options.l 2011-03-08 16:38:44.00000000= 0 +0300 +@@ -75,7 +75,7 @@ + dynamic_loops[=3D\ ][01] { ECHO; dynamic_loops =3D atoi( &yytext[14] = ); } + static_arrays[=3D\ ][01] { ECHO; static_arrays =3D atoi( &yytext[14] = ); } + blocksize[=3D\ ][0-9]+ { ECHO; blocksize =3D atoi( &yytext[10] ); } +-gbsa[=3D\ ][0-5] { ECHO; gbsa =3D atoi( &yytext[5] ); } ++gbsa[=3D\ ][01] { ECHO; gbsa =3D atoi( &yytext[5] ); } + dim[=3D\ ][34] { ECHO; dim =3D atoi( &yytext[4] ); } +=20 + rism[=3D\ ][01] { ECHO; rismData.rism =3D atoi( &yyte= xt[5] ); } +diff -urN amber11.orig/AmberTools/src/sff/sff2.c amber11/AmberTools/src/= sff/sff2.c +--- amber11.orig/AmberTools/src/sff/sff2.c 2010-03-31 07:05:17.000000000= +0400 ++++ amber11/AmberTools/src/sff/sff2.c 2011-03-08 16:38:44.000000000 +030= 0 +@@ -1384,6 +1384,7 @@ + e =3D ct2 * (ct2 * (ct2 * 32.0 - 48.0) + 18.0) - 1.0; + df =3D ct * (ct2 * (ct2 * 192.0 - 192.0) + 36.0); + ddf =3D ct2 * (ct2 * 960.0 - 576.0) + 36.0; ++ break; +=20 + default: + fprintf(stderr, "bad periodicity: %d\n", iper); +@@ -4557,7 +4558,7 @@ + qi2h =3D 0.5 * qi * qi; + qid2h =3D qi2h * dielfac; +=20 +- if ((gbsa =3D=3D 1) || (gbsa =3D=3D 4) || (gbsa =3D=3D 5)) = { ++ if ((gbsa =3D=3D 4) || (gbsa =3D=3D 5)) { + vdwdenom =3D 1.0 / (ri + rwater); + vdwterm =3D + alphanp * (prm->Gvdw[i]) * vdwdenom * vdwdenom * +diff -urN amber11.orig/AmberTools/src/sqm/qm2_load_params_and_allocate.f= amber11/AmberTools/src/sqm/qm2_load_params_and_allocate.f +--- amber11.orig/AmberTools/src/sqm/qm2_load_params_and_allocate.f 2010-= 04-14 16:13:28.000000000 +0400 ++++ amber11/AmberTools/src/sqm/qm2_load_params_and_allocate.f 2011-03-08= 16:38:44.000000000 +0300 +@@ -136,9 +136,12 @@ + n_atomic_orb=3Dnatomic_orbs(iqm_atomic) + if (n_atomic_orb>1) nheavy_atoms=3Dnheavy_atoms+1 + ! Check we don't bust any static arrays +- if (n_atomic_orb > MAX_VALENCE_ORBITALS) then +- write (6,*) 'n_atomic_orb of ',n_atomic_orb,' exceeds max_v= alence_orbitals of MAX_VALENCE_ORBITALS' +- call sander_bomb('qm2_load_params.f','exceeded max','Check = qmmm_module.f and parameters.h') ++ ! DFTB is independent of this and checks are done in qm2_dftb_= load_params ++ if ( .not. qmmm_nml%qmtheory%DFTB ) then ++ if (n_atomic_orb > MAX_VALENCE_ORBITALS) then ++ write (6,*) 'n_atomic_orb of ',n_atomic_orb,' exceeds ma= x_valence_orbitals of MAX_VALENCE_ORBITALS' ++ call sander_bomb('qm2_load_params.f','exceeded max','Che= ck qmmm_module.f and parameters.h') ++ end if + end if + qm2_params%natomic_orbs(i)=3Dn_atomic_orb + qm2_params%orb_loc(1,i)=3Dqm2_struct%norbs+1 +diff -urN amber11.orig/AmberTools/src/sqm/qm2_scf.f amber11/AmberTools/s= rc/sqm/qm2_scf.f +--- amber11.orig/AmberTools/src/sqm/qm2_scf.f 2010-03-31 07:05:17.000000= 000 +0400 ++++ amber11/AmberTools/src/sqm/qm2_scf.f 2011-03-08 16:38:44.000000000 += 0300 +@@ -33,9 +33,9 @@ + qm_gb, qmmm_mpi, qmmm_scratch + use constants, only : EV_TO_KCAL, zero, two +=20 +- use qm2_iterator_mod, only : scf_iterator_value +- use qm2_iterator_mod, only : diis_iterator_value +- use qm2_iterator_mod, only : remaining_diis_tokens ++ use qm2_iterator_mod, only : scf_iterator_value ! this is an in= teger function ++ use qm2_iterator_mod, only : diis_iterator_value ! this is an in= teger function ++ use qm2_iterator_mod, only : remaining_diis_tokens ! this is an in= teger function +=20 +=20 + implicit none +@@ -75,21 +75,24 @@ + !again. This is used to force the las= t few SCF steps to be full diagonalisations. + logical fock_predict_active !Set to true if we are attempting to pr= edict the fock matrix on this QMMM call. +=20 +- logical diis_is_off, errmat_is_converged + character(len=3D1) :: fock_extrap_flag +- logical dont_turn_off_diis +=20 ++ ! DIIS ++ ! While DIIS will accelerate SCF convergence it will do so at a ver= y high cost ++ ! since Fock matrix builds and diagonalizations for semiempirical m= ethods are ++ ! cheaper than the overhead generated by the matrix multiplications= required for DIIS ++ ! Thus switch DIIS only on if we have difficulty in converging the = SCF ++ ! switch DIIS on after SCF step 100 if user turns on DIIS by settin= g ndiis_attempts > 0 ++ integer, parameter :: switch_on_diis =3D 100 ! don't set this to va= lues lower than 3!!! ++ ! switch DIIS on as a last resort if SCF did not converge until ite= ration 800 ++ integer, parameter :: switch_on_diis_last_resort =3D 800 ++ logical diis_is_off, errmat_is_converged, errmat_is_on ++ logical dont_turn_off_diis + _REAL_ :: errval +=20 +-! scf_iterator_value is a function +-! integer :: scf_iterator_value +- + ! current_scf_errval is a function + _REAL_ :: current_scf_errval +=20 +-! remaining_diis_tokens is a function +-! integer :: remaining_diis_tokens +- + !qm2_Helect is a function + _REAL_ qm2_HELECT +=20 +@@ -141,12 +144,13 @@ + ! i =3D remaining_diis_tokens( qmmm_nml%ndiis_attempts ) + i =3D remaining_diis_tokens( 0 ) + dont_turn_off_diis =3D .FALSE. ++ diis_is_off =3D qmmm_nml%ndiis_attempts < 1 .OR. qmmm_nml%ndiis_mat= rices < 2 ++ errmat_is_on =3D qmmm_nml%errconv < 1.0D-02 ++ errval =3D -1.0D0 ! initialize errval to unrealistic value +=20 + fock_extrap_flag =3D " " +=20 +=20 +- +- + if (qmmm_nml%verbosity > 2 .and. qmmm_mpi%commqmmm_master) then + write(6,'("QMMM: ")') + write(6,'("QMMM: SCF Convergence Information")') +@@ -214,8 +218,18 @@ + energy_diff =3D scf_energy - eold +=20 + if (qmmm_mpi%commqmmm_master) then +- CALL pack_diis(SIZE(fock_matrix),fock_matrix,den_matrix) +- errval =3D current_scf_errval() ++ ! do this only if we need it, this seriously affects performan= ce ++ if ( .not. errmat_is_on ) then ++ ! check if we shall switch calculation of the error matrix = on for diis ++ if ( ( ( .not. diis_is_off ) .and. (scf_iteration+qmmm_nml%= ndiis_matrices >=3D switch_on_diis) ) & ++ .or. (scf_iteration+qmmm_nml%ndiis_matrices >=3D switc= h_on_diis_last_resort) ) then ++ errmat_is_on =3D .true. ++ end if ++ end if ++ if ( errmat_is_on ) then ++ CALL pack_diis(SIZE(fock_matrix),fock_matrix,den_matrix) ++ errval =3D current_scf_errval() ++ end if + end if +=20 +=20 +@@ -290,7 +304,7 @@ + ! IF THE USER REQUESTED US TO!! The default value of=20 + ! qmmm_nml%ndiis_attempts is 0, so this requires a form + ! of human intervention +- if ( scf_iteration =3D=3D 100 ) then ++ if ( scf_iteration =3D=3D switch_on_diis ) then + i =3D remaining_diis_tokens( qmmm_nml%ndiis_attempts ) + dont_turn_off_diis =3D .TRUE. + =20 +@@ -306,7 +320,7 @@ + ! turn the (default OFF) diis parameters on. + ! I guess we should turn diis ON for the user. + ! I mean, we're at iteration #800. What else can we do? +- if ( scf_iteration =3D=3D 800 ) then ++ if ( scf_iteration =3D=3D switch_on_diis_last_resort ) then + i =3D remaining_diis_tokens( 100 ) + dont_turn_off_diis =3D .TRUE. + =20 +@@ -329,8 +343,8 @@ + ! end if + =20 +=20 +- diis_is_off =3D qmmm_nml%ndiis_attempts < 1 .OR. qmmm_nml%nd= iis_matrices < 2 +- errmat_is_converged =3D errval < qmmm_nml%errconv !.OR. diis= _is_off ++ ! Is the error matrix converged? Set to true if we don't che= ck for the error matrix ++ errmat_is_converged =3D errval < qmmm_nml%errconv .OR. ( .no= t. errmat_is_on ) +=20 + =20 + if (abs(energy_diff) < qmmm_nml%scfconv .AND. & +@@ -379,7 +393,7 @@ + ! We have decided that we have not converged + ! We must diagonalize a fock matrix so that the next iteration can= form a new guess + ! density matrix, provided a set of trial orbitals +- if (qmmm_mpi%commqmmm_master) then ++ if (qmmm_mpi%commqmmm_master .and. (.not. diis_is_off) .and. ( scf= _iteration >=3D switch_on_diis ) ) then + CALL diis_extrap( qm2_struct%matsize, fock_matrix , fock_extrap= _flag ) + end if + =20 +@@ -1941,10 +1955,6 @@ + _REAL_,intent(out) :: pf(npf) ! packed fock matrix + character(len=3D1),intent(out) :: extrap_flag +=20 +-! integer :: scf_iterator_value +-! integer :: diis_iterator_value +-! integer :: diis_iterator_prev_value +-! integer :: remaining_diis_tokens + _REAL_ :: current_scf_errval +=20 + logical :: HAVE_DIIS_DATA +@@ -1975,7 +1985,6 @@ + ERR_IS_SMALL =3D current_scf_errval() < 0.5d0 + HAVE_DIIS_TOKENS =3D remaining_diis_tokens() > 0 + EXTRAPOLATE =3D HAVE_DIIS_DATA .AND. ERR_IS_SMALL .AND. HAVE_DII= S_TOKENS +- + IF ( .NOT. EXTRAPOLATE ) THEN + pf =3D qm2_struct%diis_fock( : , diis_idx ) + RETURN +diff -urN amber11.orig/AmberTools/src/sqm/qmmm_module.f amber11/AmberToo= ls/src/sqm/qmmm_module.f +--- amber11.orig/AmberTools/src/sqm/qmmm_module.f 2010-04-14 16:13:28.00= 0000000 +0400 ++++ amber11/AmberTools/src/sqm/qmmm_module.f 2011-03-08 16:38:44.0000000= 00 +0300 +@@ -84,7 +84,7 @@ + !--------- SIZE / ARRAY LIMITATIONS ----------------------- + =20 + ! Locks maximum valence orbitals at 4 =3D S,P (no D or F - code= is not present) +- integer, parameter :: MAX_VALENCE_ORBITALS =3D4=20 ++ integer, parameter :: MAX_VALENCE_ORBITALS =3D 4 + integer, parameter :: MAX_VALENCE_DIMENSION =3D MAX_VALENCE_ORBITALS*= (MAX_VALENCE_ORBITALS+1)/2 + =20 + !---------------------------------------------------------- +diff -urN amber11.orig/AmberTools/src/sqm/sqm.f amber11/AmberTools/src/s= qm/sqm.f +--- amber11.orig/AmberTools/src/sqm/sqm.f 2010-04-14 16:13:28.000000000 = +0400 ++++ amber11/AmberTools/src/sqm/sqm.f 2011-03-08 16:38:44.000000000 +0300 +@@ -13,7 +13,7 @@ +=20 + implicit none +=20 +- _REAL_ x(3000), f(3000), escf, reff(1000), onereff(1000), work(18000= ), scf_mchg(1000) ++ _REAL_ x(3000), f(3000), escf, reff(1000), onereff(1000), work(18000= ) + character(len=3D8) atnam(1000) + _REAL_ born_radii(1000), one_born_radii(1000) + _REAL_ intdiel, extdiel, Arad +@@ -104,20 +104,23 @@ + call allocate_qmgb(qmmm_struct%nquant_nlink) +=20 + allocate( qmmm_struct%dxyzqm(3, qmmm_struct%nquant_nlink), stat =3D = ier ) +- REQUIRE(ier =3D=3D 0) !Deallocated in deallocate qmmm ++ REQUIRE(ier =3D=3D 0) ++ ++ allocate ( qm2_struct%scf_mchg(qmmm_struct%nquant_nlink), stat =3D i= er ) ++ REQUIRE(ier =3D=3D 0) +=20 + if (maxcyc < 1) then + ! ------------------------ + ! Single point calculation + ! ------------------------ + call sqm_energy(natom, x, escf, born_radii, one_born_radii, & +- intdiel, extdiel, Arad, scf_mchg ) ++ intdiel, extdiel, Arad, qm2_struct%scf_mchg ) + else + ! --------------------- + ! Geometry optimization + ! --------------------- + call xmin(natom, x, f, escf, xmin_iter, maxcyc, born_radii, & +- one_born_radii, intdiel, extdiel, Arad, scf_mchg, grms_tol, = ntpr) ++ one_born_radii, intdiel, extdiel, Arad, qm2_struct%scf_mchg,= grms_tol, ntpr) + end if +=20 + ! ---------------- +@@ -140,7 +143,7 @@ +=20 + write(6,*) '' + call qm2_print_charges(1,qmmm_nml%dftb_chg,qmmm_struct%nquant_nlink,= & +- scf_mchg,qmmm_struct%iqm_atomic_numbers) ++ qm2_struct%scf_mchg,qmmm_struct%iqm_atomic_= numbers) +=20 + write(6,*) '' + write(6,*) 'Final Structure' +@@ -150,6 +153,12 @@ + write(6,*) ' --------- Calculation Completed ----------' + write(6,*) +=20 ++ deallocate( qmmm_struct%dxyzqm, stat =3D ier ) ++ REQUIRE(ier =3D=3D 0) ++ ++ deallocate ( qm2_struct%scf_mchg, stat =3D ier ) ++ REQUIRE(ier =3D=3D 0) ++ + call mexit(6,0) +=20 + end program sqm +diff -urN amber11.orig/AmberTools/test/check_slko_files.x amber11/AmberT= ools/test/check_slko_files.x +--- amber11.orig/AmberTools/test/check_slko_files.x 1970-01-01 03:00:00.= 000000000 +0300 ++++ amber11/AmberTools/test/check_slko_files.x 2011-03-08 16:38:44.00000= 0000 +0300 +@@ -0,0 +1,14 @@ ++#!/bin/csh -f ++#checks if cc.spl file exists - if it does then it ++#assumes that all slko files are installed. ++ ++if( -r $AMBERHOME/dat/slko/C-C.skf ) then ++ #Exists ++ exit(0) ++else ++ echo "DFTB SLKO files not found - Skipping DFTB tests..." ++ echo "" ++ exit(1) ++endif ++ ++ +diff -urN amber11.orig/AmberTools/test/nab/cuv.H1.4.dx.check amber11/Amb= erTools/test/nab/cuv.H1.4.dx.check +--- amber11.orig/AmberTools/test/nab/cuv.H1.4.dx.check 2010-04-07 16:55:= 55.000000000 +0400 ++++ amber11/AmberTools/test/nab/cuv.H1.4.dx.check 2011-03-08 16:38:44.00= 0000000 +0300 +@@ -344,7 +344,7 @@ + 0.70282E-001 0.80739E-001 0.91198E-001 + 0.94417E-001 0.91703E-001 0.77197E-001 + 0.50502E-001 0.19853E-001 -0.36599E-003 +- 0.22738E-005 0.16691E-001 0.36195E-001 ++ 0.22736E-005 0.16691E-001 0.36195E-001 + 0.49401E-001 0.53981E-001 0.53966E-001 + 0.47335E-001 0.56527E-001 0.67703E-001 + 0.78860E-001 0.90368E-001 0.10008E+000 +diff -urN amber11.orig/AmberTools/test/nab/huv.H1.4.dx.check amber11/Amb= erTools/test/nab/huv.H1.4.dx.check +--- amber11.orig/AmberTools/test/nab/huv.H1.4.dx.check 2010-04-07 16:55:= 55.000000000 +0400 ++++ amber11/AmberTools/test/nab/huv.H1.4.dx.check 2011-03-08 16:38:44.00= 0000000 +0300 +@@ -37,7 +37,7 @@ + -0.39322E-002 -0.18784E-002 -0.58137E-002 + 0.10207E-002 0.62249E-003 -0.98638E-003 + 0.37094E-003 -0.28752E-003 0.22042E-004 +- -0.99891E-004 0.15368E-003 -0.19634E-004 ++ -0.99891E-004 0.15368E-003 -0.19635E-004 + 0.35824E-003 -0.40488E-003 0.40397E-003 + 0.14213E-003 0.61945E-002 -0.76858E-002 + 0.81862E-002 -0.54091E-002 0.13352E-002 +@@ -58,7 +58,7 @@ + 0.22994E-002 -0.34751E-002 -0.37733E-001 + -0.16433E-001 -0.59317E-002 0.71093E-002 + -0.46373E-002 0.32238E-002 -0.25894E-002 +- 0.22145E-002 -0.65291E-004 -0.12695E-003 ++ 0.22145E-002 -0.65292E-004 -0.12695E-003 + -0.16873E-003 0.45506E-003 -0.14159E-002 + 0.16342E-002 -0.79582E-002 0.56556E-002 + -0.43786E-001 -0.46923E-002 -0.27685E-002 +@@ -96,11 +96,11 @@ + 0.34445E-003 0.33513E-002 0.63723E-003 + -0.45516E-003 0.16641E-004 -0.90223E-004 + 0.10300E-003 -0.99252E-004 0.15249E-004 +- -0.10662E-004 -0.19945E-004 -0.63404E-006 ++ -0.10662E-004 -0.19945E-004 -0.63406E-006 + 0.11124E-004 -0.28230E-004 -0.31534E-003 + -0.33642E-002 -0.57217E-003 -0.27793E-002 + -0.74846E-003 0.29526E-003 -0.94696E-004 +- 0.64217E-004 -0.66025E-004 -0.40449E-005 ++ 0.64216E-004 -0.66025E-004 -0.40449E-005 + -0.30799E-004 -0.16361E-004 -0.62269E-004 + -0.51020E-005 -0.16001E-003 0.92448E-004 + -0.57830E-003 -0.21012E-002 -0.69590E-003 +@@ -117,7 +117,7 @@ + -0.21378E-002 -0.44258E-003 -0.15111E-002 + -0.13934E-002 0.53131E-003 -0.22947E-003 + -0.74937E-005 -0.46655E-004 -0.61371E-004 +- 0.61593E-004 0.13955E-004 0.16010E-003 ++ 0.61594E-004 0.13955E-004 0.16010E-003 + -0.17966E-003 0.34275E-003 -0.36108E-003 + 0.76113E-003 0.23418E-002 0.29182E-003 + 0.19046E-002 0.12879E-002 -0.85274E-003 +@@ -131,7 +131,7 @@ + -0.24936E-003 0.43593E-003 -0.38975E-003 + 0.48502E-003 -0.28550E-003 0.94466E-003 + 0.27789E-002 0.71808E-003 0.38223E-002 +- -0.14124E-004 -0.13567E-002 0.12326E-002 ++ -0.14125E-004 -0.13567E-002 0.12326E-002 + -0.66934E-003 0.45864E-003 -0.28062E-003 + -0.43706E-003 0.34374E-003 -0.56160E-003 + 0.23427E-003 -0.19776E-003 -0.12917E-003 +@@ -182,7 +182,7 @@ + -0.11703E-002 0.14706E-002 -0.40144E-003 + 0.10286E-003 0.45475E-004 -0.49081E-004 + -0.47357E-004 0.54489E-006 -0.61082E-004 +- 0.65984E-004 -0.69587E-004 -0.10541E-003 ++ 0.65984E-004 -0.69588E-004 -0.10541E-003 + 0.64247E-003 0.25698E-002 0.28005E-002 + 0.27413E-002 0.12876E-002 -0.75471E-003 + 0.57492E-004 0.66448E-004 -0.42928E-004 +@@ -229,7 +229,7 @@ + -0.40783E-002 0.30972E-002 -0.35632E-002 + -0.14974E-004 0.13258E-002 -0.10864E-002 + 0.34485E-003 -0.16911E-003 -0.62126E-004 +- 0.72158E-004 -0.22208E-004 0.77266E-004 ++ 0.72158E-004 -0.22208E-004 0.77265E-004 + 0.24040E-003 -0.72533E-003 0.13593E-002 + -0.16119E-002 0.10078E-001 -0.20050E-001 + 0.72175E-002 -0.45419E-002 0.45478E-003 +@@ -292,7 +292,7 @@ + 0.33230E-003 -0.62327E-003 0.36713E-003 + -0.30819E-002 -0.32037E-003 -0.17162E-002 + -0.14580E-002 0.46999E-003 -0.97290E-004 +- -0.73333E-004 0.14729E-006 -0.11485E-003 ++ -0.73333E-004 0.14727E-006 -0.11485E-003 + -0.10058E-003 0.62528E-004 -0.17489E-003 + 0.15221E-003 -0.46879E-003 0.25396E-003 + -0.52915E-003 -0.27851E-002 0.22929E-002 +@@ -318,7 +318,7 @@ + -0.68610E-003 0.64051E-003 -0.81356E-003 + 0.24281E-003 -0.94464E-003 -0.31260E-002 + 0.48815E-002 -0.32512E-002 -0.12194E-002 +- 0.15282E-002 -0.10747E-002 0.37017E-003 ++ 0.15282E-002 -0.10747E-002 0.37016E-003 + -0.43401E-003 0.37194E-003 0.90390E-003 + -0.87376E-003 0.10045E-002 -0.10100E-002 + 0.89048E-003 -0.53634E-003 0.18096E-002 +@@ -355,14 +355,14 @@ + 0.26923E-003 -0.62333E-003 0.92867E-003 + -0.23947E-002 0.40142E-002 -0.86299E-002 + 0.45605E-002 -0.33767E-001 0.48411E-002 +- -0.86790E-002 0.13146E-002 -0.92538E-004 ++ -0.86790E-002 0.13146E-002 -0.92539E-004 + -0.33552E-003 -0.15197E-003 0.54828E-004 + -0.61954E-003 0.61334E-003 -0.71350E-003 + 0.88754E-003 -0.46185E-003 -0.11825E-002 + 0.49261E-002 -0.92336E-002 0.11674E-001 + -0.57510E-002 0.61122E-002 0.39077E-003 + -0.16127E-002 0.13002E-002 -0.76188E-003 +- 0.68127E-003 0.46393E-003 -0.60936E-003 ++ 0.68127E-003 0.46394E-003 -0.60936E-003 + 0.83803E-003 -0.13684E-002 0.18949E-002 + -0.20507E-002 0.86720E-003 0.55761E-002 + -0.38872E-002 0.87045E-002 0.57034E-003 +@@ -384,7 +384,7 @@ + 0.14459E-002 -0.36764E-002 -0.16466E-002 + 0.78190E-003 -0.21388E-003 -0.13391E-003 + -0.71292E-004 -0.25972E-004 0.81385E-005 +- -0.75784E-005 0.84210E-004 -0.57027E-004 ++ -0.75783E-005 0.84210E-004 -0.57027E-004 + 0.24646E-003 -0.15344E-004 0.44974E-003 + 0.29483E-002 -0.13186E-002 0.30172E-002 + 0.14066E-002 -0.51937E-003 0.13804E-003 +@@ -425,7 +425,7 @@ + 0.15873E-002 -0.26341E-002 0.28432E-002 + 0.49007E-003 0.10263E-001 -0.44098E-001 + 0.25985E-003 -0.50604E-002 0.20816E-002 +- -0.97801E-005 -0.13212E-003 -0.22909E-003 ++ -0.97796E-005 -0.13212E-003 -0.22909E-003 + 0.48134E-003 0.52250E-002 -0.61139E-002 + 0.74868E-002 -0.97022E-002 0.12736E-001 + -0.13924E-001 0.13569E-001 -0.16048E-001 +@@ -442,13 +442,13 @@ + -0.17468E-001 0.24222E-001 -0.13107E+000 + -0.65242E-001 0.19459E-001 -0.38769E-002 + -0.13998E-002 0.28896E-002 -0.44039E-002 +- 0.52052E-002 0.11744E-002 0.25963E-003 ++ 0.52052E-002 0.11744E-002 0.25964E-003 + -0.21866E-002 0.47172E-002 -0.81182E-002 + 0.10154E-001 -0.15684E-001 0.18417E-001 + -0.10597E+000 0.22097E-001 0.78443E-003 + -0.56097E-002 0.55039E-002 -0.44612E-002 + 0.32653E-002 -0.22953E-002 -0.13331E-002 +- 0.91243E-003 -0.94485E-004 -0.12826E-002 ++ 0.91243E-003 -0.94484E-004 -0.12826E-002 + 0.43961E-002 -0.78443E-002 0.13464E-001 + -0.13779E-002 0.40528E-001 -0.22036E-002 + 0.10425E-001 -0.96531E-003 -0.13430E-002 +@@ -512,13 +512,13 @@ + 0.11827E-001 -0.45014E-002 0.27467E-002 + -0.41543E-003 -0.71183E-003 0.52608E-003 + -0.64382E-003 0.45191E-003 0.50605E-003 +- -0.44980E-003 0.37809E-003 -0.38388E-004 ++ -0.44981E-003 0.37809E-003 -0.38389E-004 + -0.49061E-003 -0.81143E-003 0.86459E-002 + -0.45388E-002 -0.19539E-001 -0.35704E-002 +- -0.21204E-002 0.67039E-003 0.70119E-003 ++ -0.21204E-002 0.67038E-003 0.70119E-003 + -0.74427E-003 0.55233E-003 -0.45289E-003 + -0.11702E-002 0.10513E-002 -0.10446E-002 +- 0.48184E-003 -0.52832E-003 0.40688E-002 ++ 0.48184E-003 -0.52833E-003 0.40688E-002 + -0.13663E-001 -0.53287E-002 0.80893E-001 + 0.13554E-001 0.87640E-003 -0.12860E-002 + -0.94409E-003 0.13653E-002 -0.14728E-002 +@@ -570,12 +570,12 @@ + 0.55487E-003 0.57562E-002 -0.85141E-003 + 0.10230E-001 0.16214E-002 -0.31963E-002 + 0.16965E-002 -0.39151E-003 0.11883E-003 +- 0.27054E-005 -0.64436E-004 0.29371E-004 ++ 0.27053E-005 -0.64436E-004 0.29371E-004 + -0.24818E-003 0.15603E-003 -0.36597E-003 + -0.15165E-003 -0.30508E-003 -0.55843E-002 + 0.25615E-002 -0.87369E-002 -0.12896E-002 + 0.21029E-002 -0.12728E-002 0.23925E-003 +- -0.20980E-003 -0.40398E-004 -0.37869E-004 ++ -0.20980E-003 -0.40397E-004 -0.37869E-004 + -0.22762E-004 0.97304E-004 -0.13256E-003 + 0.76121E-004 0.46124E-003 -0.11364E-003 + 0.51685E-002 -0.25639E-002 0.77172E-002 +@@ -627,7 +627,7 @@ + -0.13873E-001 0.13771E-001 -0.15353E-001 + 0.19554E-001 -0.31206E-001 0.64687E-002 + 0.12878E+000 0.43115E+000 0.18311E+000 +- -0.42341E-001 0.49587E-002 0.50176E-002 ++ -0.42341E-001 0.49588E-002 0.50176E-002 + -0.10381E-001 0.12020E-001 -0.13237E-001 + -0.18428E-001 0.21596E-001 -0.25230E-001 + 0.33125E-001 -0.42929E-001 0.59353E-001 +@@ -693,12 +693,12 @@ + -0.13202E-001 -0.15081E-001 0.28654E-002 + 0.45947E-002 -0.39497E-002 0.16991E-002 + -0.85009E-003 0.46037E-003 -0.41389E-003 +- -0.11503E-004 -0.26360E-004 0.13328E-004 ++ -0.11503E-004 -0.26361E-004 0.13328E-004 + 0.44265E-003 -0.10259E-002 -0.89230E-003 + 0.43360E-002 0.12999E-001 0.67878E-002 + -0.14383E-001 -0.53637E-003 0.27114E-002 + -0.14313E-002 0.43554E-003 -0.55232E-004 +- 0.54550E-004 -0.19917E-002 0.19778E-002 ++ 0.54549E-004 -0.19917E-002 0.19778E-002 + -0.22171E-002 0.17858E-002 -0.28501E-002 + 0.81796E-002 -0.15748E-001 -0.97599E-002 + 0.11465E-001 0.41396E-001 -0.12368E-001 +@@ -737,7 +737,7 @@ + 0.33287E-001 -0.21712E-001 0.12598E-001 + -0.78119E-002 0.22442E-002 -0.20161E-001 + 0.21504E-001 -0.24273E-001 0.27271E-001 +- -0.28503E-001 0.16461E-001 -0.41419E-004 ++ -0.28503E-001 0.16461E-001 -0.41414E-004 + -0.12990E+000 0.75360E-001 -0.11560E+000 + -0.19544E-001 0.27969E-001 -0.25346E-001 + 0.21675E-001 -0.20092E-001 0.19462E-001 +@@ -766,7 +766,7 @@ + -0.47737E-003 -0.51835E-004 0.58766E-003 + -0.52596E-003 0.72315E-003 -0.11079E-001 + -0.25431E-001 -0.12595E-001 0.68054E-002 +- -0.18857E-002 0.60829E-004 0.13868E-003 ++ -0.18857E-002 0.60830E-004 0.13868E-003 + -0.55933E-003 0.34562E-003 -0.15041E-003 + 0.80074E-004 -0.32555E-003 0.67842E-003 + -0.15202E-002 0.14050E-002 -0.80795E-003 +@@ -798,7 +798,7 @@ + -0.27721E-002 0.29741E-002 -0.49061E-003 + -0.72566E-002 0.14443E-001 -0.11927E-001 + 0.82051E-001 0.95570E-002 0.10700E-002 +- -0.33922E-004 0.14627E-003 0.88681E-003 ++ -0.33919E-004 0.14627E-003 0.88681E-003 + -0.13081E-002 0.21604E-002 0.33550E-002 + -0.40840E-002 0.36977E-002 -0.35055E-002 + 0.41269E-003 0.67781E-002 0.27814E-002 +@@ -892,9 +892,9 @@ + 0.63672E-002 -0.57904E-002 0.46308E-002 + -0.36396E-002 -0.26400E-002 0.17391E-002 + -0.14131E-002 0.78246E-003 -0.61051E-003 +- 0.63366E-003 0.24693E-001 0.29656E-001 ++ 0.63365E-003 0.24693E-001 0.29656E-001 + 0.13438E+000 0.27901E-001 -0.22954E-001 +- 0.12869E-001 -0.76758E-002 0.58582E-002 ++ 0.12869E-001 -0.76757E-002 0.58582E-002 + -0.46806E-002 0.36183E-002 0.68827E-002 + -0.57133E-002 0.56860E-002 -0.66211E-002 + 0.99125E-002 -0.15797E-001 -0.52503E-002 +@@ -908,7 +908,7 @@ + -0.45900E-001 0.36916E-001 -0.30142E-001 + 0.26465E-001 0.50030E-001 -0.48827E-001 + 0.51561E-001 -0.58944E-001 0.74179E-001 +- -0.94716E-001 0.36687E-001 -0.46168E+000 ++ -0.94715E-001 0.36687E-001 -0.46168E+000 + -0.10000E+001 -0.17472E+000 0.15670E+000 + -0.98122E-001 0.78741E-001 -0.64288E-001 + 0.58448E-001 -0.52472E-001 0.59653E-001 +@@ -931,7 +931,7 @@ + -0.21260E-001 0.26058E-001 -0.35050E-001 + 0.44521E-001 -0.58930E-001 -0.46967E-002 + -0.62950E+000 -0.10000E+001 -0.58023E+000 +- 0.84660E-001 -0.20803E-001 -0.24936E-003 ++ 0.84661E-001 -0.20803E-001 -0.24937E-003 + -0.56711E-002 0.77515E-002 -0.12967E-001 + -0.33634E-001 0.36370E-001 -0.40813E-001 + 0.52730E-001 -0.69416E-001 0.11055E+000 +@@ -940,7 +940,7 @@ + -0.50993E-001 0.42341E-001 -0.35645E-001 + 0.34334E-001 0.13016E-002 -0.18908E-002 + 0.21484E-002 -0.35223E-002 0.43357E-002 +- -0.52692E-002 -0.30889E-001 -0.10458E+000 ++ -0.52692E-002 -0.30890E-001 -0.10458E+000 + 0.59570E-001 -0.10076E+000 -0.14057E-001 + 0.10367E-001 -0.60574E-002 0.13132E-002 + 0.10164E-003 -0.11144E-002 -0.80129E-003 +@@ -1070,7 +1070,7 @@ + -0.27848E-002 0.34661E-002 -0.63123E-002 + 0.10345E-001 -0.10633E-001 -0.26698E-001 + 0.37697E-001 -0.14235E-001 -0.27804E-003 +- -0.11597E-002 0.47695E-005 0.21900E-003 ++ -0.11597E-002 0.47700E-005 0.21900E-003 + -0.12610E-002 0.14246E-002 0.19513E-002 + -0.22230E-002 0.25913E-002 -0.34398E-002 + 0.62826E-002 -0.11033E-001 0.11857E-001 +@@ -1096,7 +1096,7 @@ + 0.17629E-001 -0.16578E-001 0.17704E-001 + -0.21181E-001 0.31547E-001 -0.44986E-001 + 0.53814E-001 0.61709E-001 0.41895E-001 +- -0.58391E-002 0.71644E-001 -0.50130E-001 ++ -0.58392E-002 0.71644E-001 -0.50130E-001 + 0.37052E-001 -0.27166E-001 0.23023E-001 + -0.18847E-001 -0.57070E-002 0.32394E-002 + -0.47133E-002 0.71203E-002 -0.17409E-001 +@@ -1107,7 +1107,7 @@ + 0.49908E-002 0.25980E-002 -0.10390E-001 + 0.32835E-001 -0.45644E-001 0.28388E-001 + 0.32651E+000 0.74550E+000 0.24253E-001 +- 0.23336E-001 -0.11200E-002 -0.67666E-003 ++ 0.23336E-001 -0.11200E-002 -0.67665E-003 + 0.71472E-002 -0.62491E-002 0.83474E-002 + 0.87319E-002 -0.53331E-002 -0.65393E-002 + 0.88129E-002 -0.14593E-001 -0.30915E-001 +@@ -1176,7 +1176,7 @@ + -0.12868E-002 0.13040E-002 -0.18307E-002 + 0.20870E-002 -0.20382E-002 -0.55964E-003 + 0.10698E-001 -0.18290E-001 -0.17347E-001 +- -0.20057E-001 0.63536E-002 0.17849E-002 ++ -0.20057E-001 0.63535E-002 0.17849E-002 + -0.22938E-002 0.16177E-002 -0.12481E-002 + 0.13489E-002 0.17604E-002 -0.20387E-002 + 0.25830E-002 -0.26311E-002 0.23498E-002 +@@ -1185,10 +1185,10 @@ + 0.18402E-003 0.20794E-002 -0.11926E-002 + 0.85856E-003 -0.15532E-002 -0.58085E-003 + 0.92325E-003 -0.15671E-002 0.13684E-002 +- -0.42686E-004 -0.63990E-002 0.22899E-001 ++ -0.42684E-004 -0.63990E-002 0.22899E-001 + -0.20083E-001 -0.31172E-001 -0.30073E-001 + 0.24308E-001 -0.79050E-002 0.21845E-002 +- -0.11634E-002 0.88798E-003 -0.46213E-005 ++ -0.11634E-002 0.88799E-003 -0.46216E-005 + -0.36939E-002 0.25957E-002 -0.19040E-002 + 0.22213E-002 -0.44518E-002 0.13471E-001 + -0.31065E-001 0.13930E-001 0.26443E-001 +@@ -1216,7 +1216,7 @@ + 0.12872E+000 -0.22970E+000 0.37029E-001 + -0.71820E-002 -0.61730E-002 0.60023E-002 + -0.62195E-002 0.33179E-002 0.35063E-002 +- -0.15743E-002 0.24932E-003 0.59944E-003 ++ -0.15743E-002 0.24932E-003 0.59943E-003 + 0.50805E-002 -0.22435E-001 0.78080E-001 + -0.11217E+000 0.27769E+000 0.13301E-001 + 0.48142E-001 -0.25712E-001 0.18216E-001 +@@ -1234,8 +1234,8 @@ + -0.37349E-002 0.40923E-002 0.33100E-003 + -0.73044E-003 0.14901E-002 -0.27451E-002 + 0.39569E-002 -0.39194E-002 -0.22396E-002 +- 0.69572E-002 0.15456E-001 0.68766E-003 +- -0.55836E-002 -0.59161E-004 0.28366E-003 ++ 0.69572E-002 0.15456E-001 0.68765E-003 ++ -0.55836E-002 -0.59162E-004 0.28366E-003 + 0.59373E-005 -0.29036E-003 -0.28278E-003 + -0.93105E-004 0.55976E-004 -0.22540E-003 + 0.63416E-003 -0.86325E-003 -0.56872E-003 +@@ -1259,13 +1259,13 @@ + -0.21463E-002 -0.95702E-003 0.16305E-002 + -0.48868E-003 0.37838E-003 -0.98649E-004 + 0.17415E-003 -0.39204E-003 0.40478E-003 +- -0.47636E-003 0.25159E-003 0.32794E-005 ++ -0.47636E-003 0.25159E-003 0.32795E-005 + -0.27191E-003 -0.25541E-002 0.80677E-002 + 0.23348E-001 0.22086E-002 0.10997E-002 + -0.16811E-002 0.61473E-003 -0.17759E-003 + -0.60773E-004 0.91723E-004 0.50744E-003 + -0.63597E-003 0.55533E-003 -0.33123E-003 +- -0.68908E-005 0.25682E-003 0.26735E-002 ++ -0.68909E-005 0.25682E-003 0.26735E-002 + -0.91015E-002 -0.22651E-001 -0.42938E-002 + -0.10604E-002 0.20136E-002 -0.89377E-003 + 0.20609E-003 0.28182E-004 -0.21460E-003 +@@ -1273,7 +1273,7 @@ + 0.63594E-004 0.46567E-003 -0.90712E-003 + -0.31638E-002 0.94292E-002 0.26064E-001 + 0.58926E-002 0.14824E-003 -0.26379E-002 +- 0.13364E-002 -0.27849E-003 0.67584E-007 ++ 0.13364E-002 -0.27849E-003 0.67664E-007 + 0.21329E-003 0.75173E-003 -0.70904E-003 + 0.24518E-003 -0.31473E-003 -0.44500E-003 + -0.26955E-003 0.56039E-002 -0.11484E-001 +@@ -1298,7 +1298,7 @@ + -0.74153E-002 0.51462E-002 -0.85486E-002 + 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-0.39514E-003 0.36294E-003 -0.34122E-003 +@@ -1340,7 +1340,7 @@ + -0.43384E-003 0.62665E-003 -0.53140E-003 + 0.35037E-003 0.11598E-003 -0.33590E-004 + 0.77756E-004 -0.11361E-003 0.29272E-004 +- 0.53713E-003 0.24967E-002 -0.95835E-002 ++ 0.53714E-003 0.24967E-002 -0.95835E-002 + -0.23813E-001 -0.28729E-002 0.35840E-003 + 0.75277E-003 0.14870E-003 -0.18813E-003 + 0.13874E-003 0.53665E-005 -0.82118E-004 +@@ -1383,7 +1383,7 @@ + 0.14890E-002 -0.11973E-002 0.75295E-003 + -0.10473E-002 0.10737E-002 -0.99465E-003 + 0.10667E-002 0.18484E-003 -0.15909E-002 +- -0.44370E-003 0.65566E-002 0.16554E-001 ++ -0.44371E-003 0.65566E-002 0.16554E-001 + 0.15235E-001 -0.16429E-001 0.79078E-002 + -0.29231E-002 0.16543E-002 -0.11884E-002 + 0.10008E-002 0.22131E-002 -0.11833E-002 +@@ -1395,7 +1395,7 @@ + -0.34902E-002 0.51729E-002 -0.78836E-002 + 0.96755E-002 -0.80416E-002 -0.15180E-001 + 0.48776E-001 -0.11424E+000 0.12364E-001 +- 0.32693E-002 -0.19227E-002 -0.65699E-004 ++ 0.32693E-002 -0.19227E-002 -0.65698E-004 + 0.16871E-003 0.29036E-004 -0.95792E-003 + -0.31449E-002 0.21159E-002 -0.34442E-003 + 0.30292E-003 0.22482E-002 -0.56246E-002 +@@ -1476,10 +1476,10 @@ + -0.15578E-002 0.14449E-002 -0.13015E-002 + 0.35158E-002 0.18690E-001 0.71087E-002 + -0.33624E-002 -0.86947E-004 0.13615E-002 +- -0.25872E-003 -0.28246E-003 0.49430E-003 ++ -0.25873E-003 -0.28246E-003 0.49430E-003 + 0.20061E-002 -0.22055E-002 0.25174E-002 + -0.32849E-002 0.24711E-002 -0.12430E-002 +- 0.31615E-004 -0.16073E-002 -0.13936E-001 ++ 0.31616E-004 -0.16073E-002 -0.13936E-001 + -0.78198E-002 0.10677E-001 -0.53430E-002 + 0.19467E-002 -0.20078E-002 0.18727E-002 + -0.18399E-002 -0.24069E-002 0.18144E-002 +@@ -1523,13 +1523,13 @@ + -0.57937E-004 0.38925E-004 -0.25529E-003 + -0.80223E-004 0.62244E-003 -0.92409E-003 + -0.50111E-002 -0.15028E-001 -0.48849E-002 +- 0.10809E-002 0.94785E-003 -0.90578E-003 ++ 0.10809E-002 0.94785E-003 -0.90579E-003 + 0.21632E-003 0.48547E-004 -0.10362E-003 + 0.65746E-004 -0.57485E-004 -0.10330E-003 + 0.17296E-003 -0.10843E-003 -0.17317E-003 + 0.24191E-003 0.53215E-002 0.12629E-001 + 0.39700E-002 -0.84627E-004 -0.65947E-003 +- 0.46649E-003 -0.16035E-003 0.28558E-005 ++ 0.46649E-003 -0.16035E-003 0.28557E-005 + -0.74149E-004 -0.74431E-004 0.89221E-004 + 0.14291E-004 -0.10742E-003 0.75570E-004 + 0.32302E-003 -0.45917E-003 -0.47563E-002 +@@ -1555,7 +1555,7 @@ + -0.24567E-003 0.25650E-003 -0.22210E-003 + 0.35310E-003 -0.54501E-003 0.49667E-003 + 0.46922E-002 0.53681E-003 0.53276E-002 +- -0.25038E-004 -0.47621E-003 0.25061E-003 ++ -0.25039E-004 -0.47621E-003 0.25061E-003 + -0.14151E-003 0.25689E-003 -0.23625E-003 + -0.39925E-003 0.24288E-003 -0.45878E-003 + 0.19103E-003 -0.46845E-003 0.39169E-003 +@@ -1602,7 +1602,7 @@ + -0.42312E-002 0.26362E-002 0.71520E-003 + -0.20235E-003 -0.89467E-004 0.11620E-002 + -0.32420E-002 0.52388E-002 0.58477E-003 +- -0.67996E-002 0.56024E-005 0.55241E-003 ++ -0.67996E-002 0.56018E-005 0.55241E-003 + 0.13967E-001 -0.58142E-002 0.37372E-002 + -0.25763E-002 0.19323E-002 -0.10220E-002 + -0.13957E-003 0.89996E-004 -0.29649E-003 +@@ -1726,7 +1726,7 @@ + -0.65025E-004 0.20691E-004 0.20988E-004 + 0.29987E-003 -0.69971E-003 -0.25561E-002 + -0.47408E-002 -0.17716E-002 -0.10624E-002 +- 0.72365E-003 -0.12367E-003 0.91100E-004 ++ 0.72365E-003 -0.12367E-003 0.91099E-004 + -0.11286E-003 0.65700E-004 -0.38225E-004 + -0.18443E-004 -0.10315E-004 -0.41438E-004 + -0.23530E-004 -0.27346E-003 0.79396E-003 +diff -urN amber11.orig/AmberTools/test/nab/huv.O.4.dx.check amber11/Ambe= rTools/test/nab/huv.O.4.dx.check +--- amber11.orig/AmberTools/test/nab/huv.O.4.dx.check 2010-04-07 16:55:5= 5.000000000 +0400 ++++ amber11/AmberTools/test/nab/huv.O.4.dx.check 2011-03-08 16:38:44.000= 000000 +0300 +@@ -42,10 +42,10 @@ + -0.26664E-002 0.76462E-002 -0.65646E-002 + 0.65013E-002 -0.98756E-002 0.51997E-002 + -0.15412E-002 0.14894E-002 -0.58327E-003 +- 0.74208E-003 -0.46330E-005 0.26925E-003 ++ 0.74208E-003 -0.46331E-005 0.26925E-003 + -0.21081E-003 0.19041E-003 -0.70176E-003 + 0.40604E-002 -0.59967E-002 0.25324E-001 +- -0.58949E-001 0.48671E-001 -0.63192E-002 ++ -0.58949E-001 0.48671E-001 -0.63193E-002 + -0.14555E-002 0.17515E-002 -0.12653E-002 + 0.59124E-003 -0.44081E-004 -0.46024E-003 + -0.33221E-003 0.43262E-003 -0.73462E-003 +@@ -55,10 +55,10 @@ + 0.29042E-002 -0.18964E-002 0.77617E-003 + -0.18302E-003 0.26483E-004 0.13553E-002 + -0.75012E-003 0.17059E-002 -0.70949E-003 +- 0.15620E-001 0.67864E-002 -0.96628E-001 ++ 0.15620E-001 0.67863E-002 -0.96628E-001 + -0.15238E-001 -0.64540E-002 0.11108E-001 + -0.71349E-002 0.42594E-002 -0.24297E-002 +- 0.14742E-002 0.50969E-003 -0.14490E-003 ++ 0.14742E-002 0.50969E-003 -0.14489E-003 + -0.15852E-002 0.26525E-002 -0.54371E-002 + 0.63513E-002 -0.19991E-001 0.88607E-003 + -0.90619E-001 -0.26234E-001 0.54685E-002 +@@ -74,7 +74,7 @@ + -0.67192E-002 0.20436E-002 0.15087E-002 + -0.12351E-001 -0.10538E-001 0.30347E-002 + -0.24133E-002 0.57521E-003 -0.89346E-003 +- -0.19758E-003 0.85846E-004 0.21885E-003 ++ -0.19759E-003 0.85846E-004 0.21885E-003 + 0.59427E-004 0.40476E-003 -0.45294E-003 + 0.17127E-002 0.22700E-002 -0.36055E-002 + -0.94861E-002 -0.31257E-002 0.59927E-002 +@@ -89,13 +89,13 @@ + -0.21190E-003 0.38823E-003 -0.99192E-004 + 0.14844E-002 -0.48467E-002 -0.10472E-001 + -0.56834E-002 0.17312E-002 0.44869E-003 +- 0.59430E-004 -0.99269E-004 0.22702E-003 ++ 0.59429E-004 -0.99269E-004 0.22702E-003 + -0.46728E-004 -0.99733E-004 -0.59632E-005 + -0.15996E-003 0.21334E-003 -0.60938E-003 + 0.46539E-003 -0.16741E-002 0.53916E-002 + 0.73981E-002 0.59857E-002 -0.16663E-002 + 0.12223E-003 -0.48450E-003 0.17812E-003 +- -0.11241E-003 -0.53881E-005 0.24248E-003 ++ -0.11241E-003 -0.53882E-005 0.24248E-003 + -0.20069E-003 0.17999E-003 -0.24877E-003 + 0.30370E-003 -0.44718E-003 0.73307E-003 + -0.42363E-002 -0.80946E-002 -0.48617E-002 +@@ -172,7 +172,7 @@ + 0.18498E-002 -0.73133E-003 0.88568E-003 + -0.14499E-003 -0.13914E-004 -0.23519E-003 + 0.28978E-003 -0.69524E-003 0.99658E-003 +- -0.19354E-002 -0.38389E-003 -0.15309E-003 ++ -0.19354E-002 -0.38389E-003 -0.15308E-003 + 0.11672E-001 0.37757E-002 -0.51548E-002 + -0.91017E-003 0.87189E-003 -0.57806E-003 + 0.16146E-003 -0.22842E-003 0.37037E-004 +@@ -181,7 +181,7 @@ + -0.96518E-003 -0.13418E-001 -0.54575E-002 + 0.20411E-002 0.10281E-002 -0.33249E-003 + 0.17999E-003 0.19469E-003 0.23293E-004 +- -0.45970E-005 -0.10166E-003 0.26448E-004 ++ -0.45969E-005 -0.10166E-003 0.26448E-004 + -0.60871E-004 0.21195E-003 -0.53324E-003 + 0.48474E-003 0.57259E-003 0.14242E-001 + 0.41534E-002 -0.65370E-003 -0.53279E-003 +@@ -259,7 +259,7 @@ + 0.23319E-002 -0.18642E-002 0.17647E-002 + -0.49400E-003 0.48144E-003 0.46341E-002 + 0.17097E-001 0.13221E-001 0.13122E-001 +- 0.88689E-002 -0.14616E-002 0.73569E-004 ++ 0.88689E-002 -0.14616E-002 0.73570E-004 + 0.16176E-002 -0.17425E-002 0.23255E-002 + 0.10067E-002 -0.10794E-002 0.61036E-003 + -0.79346E-003 -0.18114E-003 0.10066E-002 +@@ -296,7 +296,7 @@ + -0.79564E-003 0.73627E-003 -0.10642E-002 + 0.89864E-003 -0.15015E-002 0.74366E-003 + -0.10995E-002 -0.91302E-003 -0.14389E-002 +- -0.62659E-002 0.16322E-003 0.39747E-003 ++ -0.62659E-002 0.16322E-003 0.39746E-003 + -0.93576E-003 0.27055E-003 -0.70408E-003 + 0.55227E-003 0.91932E-003 -0.80784E-003 + 0.10504E-002 -0.99128E-003 0.13799E-002 +@@ -333,7 +333,7 @@ + 0.11332E-002 -0.36329E-002 0.45738E-002 + -0.64277E-002 0.84257E-002 -0.10759E-001 + 0.10170E-001 -0.10632E-001 -0.65535E-002 +- 0.50679E-001 -0.70621E-001 0.91916E-002 ++ 0.50679E-001 -0.70621E-001 0.91917E-002 + 0.32587E-002 -0.38023E-002 0.34644E-002 + -0.32950E-002 0.30559E-002 -0.13480E-003 + 0.19650E-002 -0.34448E-002 0.59077E-002 +@@ -364,7 +364,7 @@ + 0.19684E-002 -0.10859E-002 0.12621E-002 + -0.43675E-003 0.74924E-003 -0.10527E-002 + 0.16471E-002 -0.24027E-002 0.31736E-002 +- -0.29570E-002 -0.47347E-004 -0.17740E-002 ++ -0.29570E-002 -0.47348E-004 -0.17740E-002 + 0.12840E-002 0.13132E-001 -0.86557E-002 + -0.65506E-003 0.21598E-002 -0.13016E-002 + 0.84158E-003 -0.68238E-003 -0.21792E-003 +@@ -387,7 +387,7 @@ + -0.60950E-003 0.93571E-003 -0.76457E-003 + 0.12784E-002 -0.70392E-003 0.15756E-002 + -0.13275E-003 0.45733E-002 0.69172E-002 +- -0.41320E-003 -0.14128E-004 0.54688E-003 ++ -0.41320E-003 -0.14127E-004 0.54688E-003 + -0.19076E-004 0.49968E-003 -0.38501E-003 + 0.43234E-003 -0.22011E-003 -0.83980E-005 + 0.30076E-003 -0.68470E-003 0.24934E-002 +@@ -507,13 +507,13 @@ + 0.78218E-002 -0.41701E-002 -0.79742E-003 + 0.32867E-002 -0.37463E-002 0.34769E-002 + -0.26528E-002 -0.24349E-002 0.21354E-002 +- -0.24623E-002 0.90930E-003 0.54718E-003 ++ -0.24623E-002 0.90930E-003 0.54717E-003 + -0.17165E-002 0.28721E-003 -0.10121E-001 + 0.35717E-001 -0.26042E-002 0.34331E-002 + -0.19519E-003 -0.26581E-002 0.27915E-002 + -0.33505E-002 0.24742E-002 0.26514E-002 + -0.19360E-002 0.14202E-002 -0.31884E-003 +- -0.74542E-003 -0.87196E-003 0.41982E-002 ++ -0.74541E-003 -0.87196E-003 0.41982E-002 + 0.13483E-001 -0.64738E-001 -0.11160E-001 + 0.55671E-003 -0.98428E-003 0.33064E-002 + -0.35116E-002 0.31262E-002 -0.26684E-002 +@@ -524,7 +524,7 @@ + -0.22229E-002 0.28090E-002 -0.29004E-002 + 0.20027E-002 -0.27248E-002 0.44242E-002 + -0.69761E-002 0.87857E-002 -0.91317E-002 +- 0.23035E-002 -0.51691E-002 0.21490E-001 ++ 0.23035E-002 -0.51692E-002 0.21490E-001 + -0.37282E-001 -0.18265E+000 0.58260E-001 + -0.16382E-001 0.57561E-002 -0.21236E-002 + 0.14273E-003 0.11916E-002 0.90109E-003 +@@ -556,7 +556,7 @@ + 0.12840E-001 -0.78465E-002 0.66047E-002 + -0.46569E-002 0.17062E-002 -0.20716E-002 + 0.25710E-002 -0.29188E-002 0.15776E-002 +- 0.10926E-002 -0.65054E-002 -0.64167E-004 ++ 0.10926E-002 -0.65054E-002 -0.64166E-004 + 0.42370E-002 0.33049E-001 -0.26709E-001 + 0.72769E-002 -0.60839E-004 -0.13599E-002 + 0.14205E-002 -0.14190E-002 -0.17898E-002 +@@ -589,7 +589,7 @@ + -0.11534E-002 -0.28262E-003 -0.41205E-003 + 0.12794E-002 -0.27790E-002 0.41709E-002 + -0.68711E-002 0.84175E-002 -0.75839E-002 +- -0.28437E-001 0.50508E-003 0.41340E-002 ++ -0.28437E-001 0.50507E-003 0.41340E-002 + -0.61449E-003 -0.18493E-002 0.12523E-002 + -0.11168E-002 0.69345E-003 -0.83917E-004 + 0.57404E-003 -0.17705E-002 0.28814E-002 +@@ -611,14 +611,14 @@ + -0.13675E-002 0.26363E-002 -0.43034E-002 + 0.41848E-002 0.12480E-002 -0.36641E-002 + -0.34640E-001 0.87778E-001 0.58409E-001 +- -0.21333E-001 0.74525E-002 -0.48739E-002 ++ -0.21333E-001 0.74524E-002 -0.48739E-002 + 0.30753E-002 -0.18387E-002 0.69893E-003 +- 0.71286E-003 0.44580E-003 -0.24335E-002 +- 0.43811E-002 -0.38330E-002 -0.13636E-002 ++ 0.71285E-003 0.44580E-003 -0.24335E-002 ++ 0.43812E-002 -0.38330E-002 -0.13635E-002 + -0.13480E-001 0.11325E+000 -0.29436E+000 + -0.10004E+000 0.41518E-001 -0.16200E-001 + 0.94931E-002 -0.61992E-002 0.43081E-002 +- -0.25405E-002 -0.34159E-002 0.55821E-003 ++ -0.25405E-002 -0.34159E-002 0.55820E-003 + 0.27477E-002 -0.42526E-002 0.30568E-002 + 0.47572E-002 0.23098E-001 -0.11741E+000 + 0.20977E+000 0.38183E+000 -0.15864E+000 +@@ -640,11 +640,11 @@ + -0.21429E+000 -0.70469E-001 0.64050E-001 + -0.48755E-001 0.39460E-001 -0.31552E-001 + 0.27718E-001 -0.23853E-001 -0.11746E-002 +- -0.76642E-004 0.19535E-002 -0.28967E-002 ++ -0.76641E-004 0.19535E-002 -0.28967E-002 + 0.23194E-002 0.14434E-001 -0.39994E-001 + 0.20057E+000 -0.14250E+000 0.15546E+000 + -0.10132E-001 -0.19003E-002 0.31489E-002 +- -0.13663E-003 -0.61045E-003 0.13419E-002 ++ -0.13663E-003 -0.61046E-003 0.13419E-002 + -0.56599E-002 0.65318E-002 -0.99441E-002 + 0.14290E-001 -0.21240E-001 0.25559E-001 + -0.26500E-001 -0.45351E-001 0.12464E+000 +@@ -654,7 +654,7 @@ + -0.67183E-003 -0.17567E-002 0.59214E-002 + -0.10795E-001 0.19998E-001 0.21432E-003 + -0.57072E-001 -0.26436E-001 0.40361E-001 +- -0.15950E-001 0.39954E-002 0.38634E-004 ++ -0.15950E-001 0.39954E-002 0.38633E-004 + -0.19542E-002 0.20302E-002 0.41282E-002 + -0.37590E-002 0.25828E-002 -0.18860E-002 + 0.84274E-003 0.59538E-003 -0.40063E-002 +@@ -695,7 +695,7 @@ + 0.36780E-002 -0.41785E-002 0.43203E-002 + 0.67542E-002 -0.67533E-002 0.79253E-002 + -0.75232E-002 0.71990E-002 -0.10331E-001 +- 0.88066E-002 0.69559E-002 0.27927E-001 ++ 0.88065E-002 0.69559E-002 0.27927E-001 + -0.45171E-001 0.11785E-001 -0.37993E-002 + 0.44794E-002 -0.60610E-002 0.70033E-002 + -0.62684E-002 -0.97638E-002 0.97810E-002 +@@ -730,7 +730,7 @@ + -0.28215E+000 0.56642E+000 0.92065E+000 + 0.10006E+001 -0.46958E+000 0.29382E+000 + -0.20618E+000 0.16462E+000 -0.13004E+000 +- 0.10753E+000 -0.15069E-002 0.65807E-003 ++ 0.10753E+000 -0.15069E-002 0.65808E-003 + -0.59134E-002 0.17916E-001 -0.43687E-001 + 0.85179E-001 -0.72107E-001 0.17888E+000 + 0.27398E+000 0.17046E+000 -0.12239E+000 +@@ -805,7 +805,7 @@ + -0.92333E-001 -0.73061E-001 -0.12402E+000 + 0.49643E-001 -0.24501E-001 0.12081E-001 + -0.77686E-002 0.65912E-002 -0.68733E-002 +- -0.52386E-001 0.55294E-001 -0.60917E-001 ++ -0.52386E-001 0.55294E-001 -0.60918E-001 + 0.72284E-001 -0.90668E-001 0.13640E+000 + -0.30725E+000 0.68114E+000 -0.63520E+000 + 0.69895E+000 -0.30705E+000 0.16706E+000 +@@ -815,7 +815,7 @@ + -0.16169E+000 0.42947E+000 -0.10000E+001 + -0.10000E+001 -0.10000E+001 0.34773E+000 + -0.16448E+000 0.95838E-001 -0.65437E-001 +- 0.53108E-001 -0.49594E-001 0.10228E-004 ++ 0.53108E-001 -0.49594E-001 0.10227E-004 + -0.83130E-002 0.19382E-001 -0.43694E-001 + 0.82990E-001 -0.15068E+000 0.19264E+000 + -0.10000E+001 -0.10000E+001 -0.10000E+001 +@@ -853,7 +853,7 @@ + -0.15840E+000 0.15063E+000 -0.97388E-001 + -0.22784E-002 0.85043E-002 -0.62997E-002 + 0.44880E-002 -0.39095E-002 0.45371E-002 +- 0.70889E-004 -0.68019E-003 0.59256E-003 ++ 0.70888E-004 -0.68019E-003 0.59256E-003 + -0.84557E-004 -0.36226E-002 0.15213E-001 + -0.31110E-001 0.13861E+000 -0.15051E+000 + 0.81020E-001 -0.11901E-001 0.36571E-002 +@@ -880,10 +880,10 @@ + -0.36432E+000 0.48476E-001 -0.13337E-001 + -0.85939E-003 0.62937E-002 -0.90302E-002 + 0.96864E-002 -0.10054E-001 -0.12074E-001 +- 0.12686E-001 -0.13788E-001 0.15535E-001 ++ 0.12686E-001 -0.13788E-001 0.15534E-001 + -0.12609E-001 0.43721E-002 0.38811E-001 + -0.54071E-002 0.36037E+000 -0.26901E-001 +- -0.91861E-004 0.75691E-002 -0.10423E-001 ++ -0.91871E-004 0.75691E-002 -0.10423E-001 + 0.13325E-001 -0.12466E-001 0.12184E-001 + 0.16486E-001 -0.16264E-001 0.18217E-001 + -0.18145E-001 0.15178E-001 -0.90728E-002 +@@ -943,7 +943,7 @@ + -0.29396E-001 -0.11815E-001 -0.23817E+000 + -0.18515E+000 -0.25452E+000 0.27722E-001 + 0.16855E-002 -0.72308E-002 0.20876E-002 +- 0.64586E-003 -0.38825E-002 0.21534E-002 ++ 0.64585E-003 -0.38825E-002 0.21535E-002 + 0.21199E-003 -0.19208E-002 0.42601E-002 + -0.22560E-002 -0.69878E-002 0.71728E-001 + 0.78877E-002 0.44965E+000 -0.21828E-001 +@@ -1064,7 +1064,7 @@ + 0.62403E-002 -0.60207E-002 0.73668E-002 + -0.70398E-002 0.11315E-001 -0.95645E-002 + -0.32328E-002 0.87432E-001 -0.15443E+000 +- 0.46011E-001 -0.18490E-003 -0.10438E-003 ++ 0.46011E-001 -0.18489E-003 -0.10438E-003 + 0.37293E-002 -0.27929E-002 0.52303E-002 + -0.50491E-002 -0.64016E-002 0.64120E-002 + -0.66729E-002 0.70889E-002 -0.10324E-001 +@@ -1089,7 +1089,7 @@ + -0.29061E-001 0.21213E-001 -0.17088E-001 + 0.15692E-001 -0.12454E-001 -0.16919E-001 + 0.14774E-001 -0.13566E-001 0.14799E-001 +- -0.20251E-001 0.21467E-001 0.51689E-002 ++ -0.20251E-001 0.21467E-001 0.51690E-002 + -0.17781E+000 0.16897E+000 -0.17823E-001 + -0.62278E-001 0.48487E-001 -0.35890E-001 + 0.27828E-001 -0.25327E-001 0.20069E-001 +@@ -1107,7 +1107,7 @@ + -0.22781E-001 0.41204E-001 -0.58124E-001 + 0.92982E-001 -0.99577E-001 0.51029E-001 + 0.38111E+000 0.12849E+001 -0.41711E-001 +- 0.46704E-001 -0.59395E-002 0.38283E-002 ++ 0.46704E-001 -0.59395E-002 0.38284E-002 + 0.24958E-002 0.34276E-002 -0.52601E-002 + -0.10267E-001 0.31273E-001 -0.64242E-001 + 0.80909E-001 -0.99093E-001 0.32420E-001 +@@ -1144,13 +1144,13 @@ + -0.40730E-002 0.49874E-002 -0.73690E-002 + 0.73535E-002 -0.95872E-002 0.77701E-002 + 0.63260E-002 -0.93757E-001 0.13558E+000 +- -0.89965E-001 0.17086E-001 -0.10569E-001 ++ -0.89964E-001 0.17086E-001 -0.10569E-001 + 0.42904E-002 -0.19884E-002 -0.52517E-003 + 0.16988E-002 0.51231E-002 -0.58474E-002 + 0.72663E-002 -0.82602E-002 0.11856E-001 + -0.10246E-001 -0.30199E-002 0.86203E-001 + -0.14974E+000 0.68805E-001 -0.10227E-001 +- 0.55756E-002 -0.95949E-004 -0.69091E-003 ++ 0.55756E-002 -0.95950E-004 -0.69091E-003 + 0.22362E-002 -0.35971E-002 -0.60713E-002 + 0.60472E-002 -0.79022E-002 0.78322E-002 + -0.12783E-001 0.10462E-001 0.31255E-002 +@@ -1260,7 +1260,7 @@ + 0.10679E-002 -0.90389E-003 0.16602E-002 + -0.11913E-002 -0.20977E-002 0.20942E-002 + -0.18004E-002 0.16284E-002 -0.18577E-002 +- 0.22835E-002 -0.67831E-002 0.25191E-004 ++ 0.22835E-002 -0.67831E-002 0.25192E-004 + 0.76945E-001 -0.45030E-002 -0.18644E-002 + -0.90606E-004 -0.93679E-003 0.16082E-002 + -0.17131E-002 0.17442E-002 0.26104E-002 +@@ -1381,7 +1381,7 @@ + 0.69183E-002 -0.44728E-001 -0.18229E-001 + 0.19727E-001 -0.83985E-002 0.19649E-002 + -0.81000E-003 0.18733E-002 -0.62522E-003 +- -0.12105E-002 -0.72607E-005 0.89095E-003 ++ -0.12105E-002 -0.72605E-005 0.89095E-003 + -0.15643E-002 0.48042E-002 -0.83264E-002 + 0.65796E-002 -0.21426E-001 0.49776E-001 + 0.39843E-002 -0.24431E-001 0.15999E-001 +@@ -1414,7 +1414,7 @@ + 0.23073E-001 -0.17327E-001 0.14432E-001 + -0.10868E-001 0.93471E-002 -0.68998E-002 + -0.26163E-002 0.31335E-002 -0.16844E-002 +- -0.29736E-003 0.27007E-002 -0.34378E-002 ++ -0.29736E-003 0.27007E-002 -0.34377E-002 + -0.10124E-001 0.16906E-001 -0.27972E-001 + -0.46722E-001 -0.99915E-002 0.74033E-002 + -0.49759E-002 0.33691E-002 -0.30633E-002 +@@ -1490,7 +1490,7 @@ + 0.56865E-003 -0.25998E-002 0.23230E-003 + -0.48411E-003 0.19935E-002 -0.43491E-002 + 0.86658E-002 -0.20913E-001 0.67877E-001 +- -0.12506E+000 0.30915E+000 -0.45000E-001 ++ -0.12506E+000 0.30915E+000 -0.45001E-001 + 0.79047E-002 -0.21891E-003 -0.32671E-003 + -0.91926E-003 0.50793E-003 0.11241E-003 + 0.15086E-001 -0.89428E-002 -0.35368E-003 +@@ -1507,7 +1507,7 @@ + -0.30669E-003 -0.89002E-003 -0.12172E-002 + 0.45842E-002 -0.33508E-002 -0.14322E-001 + 0.66905E-002 0.40619E-001 -0.51873E-001 +- -0.65372E-002 0.52189E-002 -0.46499E-002 ++ -0.65372E-002 0.52190E-002 -0.46499E-002 + 0.43349E-002 -0.38558E-002 0.59891E-003 + 0.34349E-003 -0.86951E-003 0.19112E-002 + -0.11810E-002 -0.18282E-002 0.31268E-002 +@@ -1524,7 +1524,7 @@ + 0.12391E-003 -0.17626E-003 0.37440E-002 + -0.73418E-002 -0.43798E-001 0.49519E-002 + 0.14953E-002 0.20774E-002 -0.22890E-002 +- 0.11235E-002 0.53678E-004 0.34160E-004 ++ 0.11235E-002 0.53679E-004 0.34160E-004 + -0.92654E-003 0.75587E-003 -0.15990E-002 + 0.13713E-002 -0.14112E-002 0.18715E-002 + -0.44715E-002 0.85039E-002 0.41635E-001 +@@ -1534,13 +1534,13 @@ + 0.11901E-002 -0.16300E-002 0.17072E-002 + -0.20384E-002 0.41606E-002 -0.83538E-002 + -0.36935E-001 -0.18397E-003 0.75164E-003 +- 0.32749E-004 -0.54313E-004 -0.55384E-003 ++ 0.32749E-004 -0.54314E-004 -0.55384E-003 + 0.59897E-003 -0.55366E-003 -0.85402E-003 + 0.60344E-003 -0.12434E-002 0.99286E-003 + -0.13524E-002 0.82954E-003 -0.21224E-002 + 0.41911E-002 0.38989E-001 -0.21565E-002 + 0.91862E-003 -0.97115E-003 0.27219E-003 +- 0.52312E-005 -0.71291E-003 0.34833E-003 ++ 0.52313E-005 -0.71291E-003 0.34833E-003 + -0.48047E-003 0.23123E-003 -0.44657E-003 + 0.33067E-003 -0.41250E-003 0.10632E-003 + -0.22842E-002 0.73852E-002 0.61030E-002 +@@ -1574,7 +1574,7 @@ + 0.99674E-002 -0.24989E-002 0.30342E-003 + -0.53277E-003 0.79955E-003 -0.21966E-003 + -0.59661E-003 0.35264E-003 -0.65872E-004 +- 0.11436E-002 0.38480E-003 -0.35781E-002 ++ 0.11436E-002 0.38479E-003 -0.35781E-002 + 0.36223E-002 -0.75229E-002 0.15451E-001 + 0.40636E-002 -0.14021E-001 0.68264E-002 + -0.25865E-002 0.28621E-002 -0.14937E-002 +@@ -1607,7 +1607,7 @@ + -0.72048E-002 0.52170E-002 -0.32634E-002 + -0.19081E-002 0.22332E-002 -0.24117E-002 + 0.23217E-002 0.50866E-003 -0.17204E-002 +- -0.75871E-002 0.73309E-002 0.25632E-005 ++ -0.75871E-002 0.73309E-002 0.25651E-005 + -0.21416E-001 -0.12367E-001 0.49953E-002 + -0.41626E-002 0.41883E-002 -0.30311E-002 + 0.19037E-002 0.31388E-003 -0.26396E-003 +@@ -1640,8 +1640,8 @@ + 0.33179E-003 -0.34087E-003 0.23211E-003 + -0.32071E-003 -0.56331E-004 0.14792E-003 + -0.41476E-003 -0.10262E-002 -0.21101E-001 +- -0.94099E-004 -0.10972E-002 0.73413E-003 +- -0.43772E-003 -0.10434E-003 0.72385E-004 ++ -0.94100E-004 -0.10972E-002 0.73413E-003 ++ -0.43772E-003 -0.10434E-003 0.72384E-004 + -0.27691E-003 -0.27499E-003 0.40064E-003 + -0.26074E-003 0.46773E-003 -0.13622E-003 + 0.20913E-003 -0.18338E-003 0.73660E-003 +@@ -1683,7 +1683,7 @@ + 0.38887E-003 -0.10225E-003 -0.35480E-003 + 0.21989E-002 -0.46306E-002 0.27804E-001 + -0.46260E-001 0.99268E-001 -0.12849E-001 +- 0.69339E-002 -0.28353E-002 0.32796E-002 ++ 0.69340E-002 -0.28353E-002 0.32796E-002 + -0.19358E-002 0.10950E-002 -0.18272E-003 + 0.56051E-002 -0.38298E-002 0.13655E-003 + 0.13715E-002 -0.54991E-002 0.85791E-002 +diff -urN amber11.orig/AmberTools/test/nab/Makefile amber11/AmberTools/t= est/nab/Makefile +--- amber11.orig/AmberTools/test/nab/Makefile 2010-04-01 08:14:34.000000= 000 +0400 ++++ amber11/AmberTools/test/nab/Makefile 2011-03-08 16:38:44.000000000 += 0300 +@@ -12,7 +12,7 @@ + rattle_md_test rembed_test dhfrndpmtx_test asp_test \ + aspnb_test prm_test cif_test xmin_test \ + lmod_test nmode1_test nmode2_test nmode3_test ips_test \ +- pbsa_test rism_test rism_md_test rism_dist rism_hnc ++ pbsa_test rism_test rism_md_test rism_dist rism_hnc rism_ion +=20 + duplex_test:: + @./Run.duplex +@@ -112,3 +112,6 @@ +=20 + rism_dist:: + @./Run.rism_dist ++ ++rism_ion:: ++ @sh ./Run.rism_ion +diff -urN amber11.orig/AmberTools/test/nab/Na+.parm7 amber11/AmberTools/= test/nab/Na+.parm7 +--- amber11.orig/AmberTools/test/nab/Na+.parm7 1970-01-01 03:00:00.00000= 0000 +0300 ++++ amber11/AmberTools/test/nab/Na+.parm7 2011-03-08 16:38:44.000000000 = +0300 +@@ -0,0 +1,124 @@ ++%VERSION VERSION_STAMP =3D V0001.000 DATE =3D 06/20/07 15:21:17 = =20 ++%FLAG TITLE = =20 ++%FORMAT(20a4) = =20 ++ = =20 ++%FLAG POINTERS = =20 ++%FORMAT(10I8) = =20 ++ 1 1 0 0 0 0 0 0 = 0 0 ++ 1 1 0 0 0 0 0 0 = 1 0 ++ 0 0 0 0 0 0 0 1 = 1 0 ++ 0 ++%FLAG ATOM_NAME = =20 ++%FORMAT(20a4) = =20 ++Na+=20 ++%FLAG CHARGE = =20 ++%FORMAT(5E16.8) = =20 ++ 1.82223000E+01 ++%FLAG MASS = =20 ++%FORMAT(5E16.8) = =20 ++ 2.29900000E+01 ++%FLAG ATOM_TYPE_INDEX = =20 ++%FORMAT(10I8) = =20 ++ 1 ++%FLAG NUMBER_EXCLUDED_ATOMS = =20 ++%FORMAT(10I8) = =20 ++ 1 ++%FLAG NONBONDED_PARM_INDEX = =20 ++%FORMAT(10I8) = =20 ++ 1 ++%FLAG RESIDUE_LABEL = =20 ++%FORMAT(20a4) = =20 ++Na+=20 ++%FLAG RESIDUE_POINTER = =20 ++%FORMAT(10I8) = =20 ++ 1 ++%FLAG BOND_FORCE_CONSTANT = =20 ++%FORMAT(5E16.8) = =20 ++ ++%FLAG BOND_EQUIL_VALUE = =20 ++%FORMAT(5E16.8) = =20 ++ ++%FLAG ANGLE_FORCE_CONSTANT = =20 ++%FORMAT(5E16.8) = =20 ++ ++%FLAG ANGLE_EQUIL_VALUE = =20 ++%FORMAT(5E16.8) = =20 ++ ++%FLAG DIHEDRAL_FORCE_CONSTANT = =20 ++%FORMAT(5E16.8) = =20 ++ ++%FLAG DIHEDRAL_PERIODICITY = =20 ++%FORMAT(5E16.8) = =20 ++ ++%FLAG DIHEDRAL_PHASE = =20 ++%FORMAT(5E16.8) = =20 ++ ++%FLAG SOLTY = =20 ++%FORMAT(5E16.8) = =20 ++ 0.00000000E+00 ++%FLAG LENNARD_JONES_ACOEF = =20 ++%FORMAT(5E16.8) = =20 ++ 2.04815198E+04 ++%FLAG LENNARD_JONES_BCOEF = =20 ++%FORMAT(5E16.8) = =20 ++ 1.50643699E+01 ++%FLAG BONDS_INC_HYDROGEN = =20 ++%FORMAT(10I8) = =20 ++ ++%FLAG BONDS_WITHOUT_HYDROGEN = =20 ++%FORMAT(10I8) = =20 ++ ++%FLAG ANGLES_INC_HYDROGEN = =20 ++%FORMAT(10I8) = =20 ++ ++%FLAG ANGLES_WITHOUT_HYDROGEN = =20 ++%FORMAT(10I8) = =20 ++ ++%FLAG DIHEDRALS_INC_HYDROGEN = =20 ++%FORMAT(10I8) = =20 ++ ++%FLAG DIHEDRALS_WITHOUT_HYDROGEN = =20 ++%FORMAT(10I8) = =20 ++ ++%FLAG EXCLUDED_ATOMS_LIST = =20 ++%FORMAT(10I8) = =20 ++ 0 ++%FLAG HBOND_ACOEF = =20 ++%FORMAT(5E16.8) = =20 ++ ++%FLAG HBOND_BCOEF = =20 ++%FORMAT(5E16.8) = =20 ++ ++%FLAG HBCUT = =20 ++%FORMAT(5E16.8) = =20 ++ ++%FLAG AMBER_ATOM_TYPE = =20 ++%FORMAT(20a4) = =20 ++IP =20 ++%FLAG TREE_CHAIN_CLASSIFICATION = =20 ++%FORMAT(20a4) = =20 ++M =20 ++%FLAG JOIN_ARRAY = =20 ++%FORMAT(10I8) = =20 ++ 0 ++%FLAG IROTAT = =20 ++%FORMAT(10I8) = =20 ++ 0 ++%FLAG SOLVENT_POINTERS = =20 ++%FORMAT(3I8) = =20 ++ 1 1 2 ++%FLAG ATOMS_PER_MOLECULE = =20 ++%FORMAT(10I8) = =20 ++ 1 ++%FLAG BOX_DIMENSIONS = =20 ++%FORMAT(5E16.8) = =20 ++ 9.00000000E+01 2.56000000E+01 2.56000000E+01 2.56000000E+01 ++%FLAG RADIUS_SET = =20 ++%FORMAT(1a80) = =20 ++modified Bondi radii (mbondi) = =20 ++%FLAG RADII = =20 ++%FORMAT(5E16.8) = =20 ++ 1.50000000E+00 ++%FLAG SCREEN = =20 ++%FORMAT(5E16.8) = =20 ++ 8.00000000E-01 +diff -urN amber11.orig/AmberTools/test/nab/Na+.pdb amber11/AmberTools/te= st/nab/Na+.pdb +--- amber11.orig/AmberTools/test/nab/Na+.pdb 1970-01-01 03:00:00.0000000= 00 +0300 ++++ amber11/AmberTools/test/nab/Na+.pdb 2011-03-08 16:38:44.000000000 +0= 300 +@@ -0,0 +1,4 @@ ++REMARK =20 ++ATOM 1 Na+ Na+ 1 0.000 0.000 0.000 1.00 0.00 = N =20 ++TER =20 ++END =20 +diff -urN amber11.orig/AmberTools/test/nab/rismion.nab amber11/AmberTool= s/test/nab/rismion.nab +--- amber11.orig/AmberTools/test/nab/rismion.nab 1970-01-01 03:00:00.000= 000000 +0300 ++++ amber11/AmberTools/test/nab/rismion.nab 2011-03-08 16:38:44.00000000= 0 +0300 +@@ -0,0 +1,22 @@ ++molecule m; ++float m_xyz[dynamic], f_xyz[dynamic], v_xyz[dynamic]; ++float dgrad, fret; ++int ier, i;=20 ++ ++m =3D getpdb("Na+.pdb"); ++readparm(m, "Na+.parm7"); ++allocate m_xyz[3*m.natoms]; ++allocate f_xyz[3*m.natoms]; ++allocate v_xyz[3*m.natoms]; ++mm_options( "e_debug=3D0, ntpr=3D1, ntpr_md=3D1, cut=3D999.0, dt=3D0.00= 1, rattle=3D0, tempi=3D0, zerov=3D0"); ++mm_options( "rism=3D1, apply_rism_force=3D0"); ++mm_options( "buffer=3D12, solvcut=3D999"); ++mm_options( "progress=3D1, xvvfile=3D../rism1d/spc/spc-nacl.xvv.save"); ++mme_init( m, NULL, "::Z", m_xyz, NULL); ++ ++setxyz_from_mol( m, NULL, m_xyz ); ++ ++ier =3D md(3*m.natoms,0,m_xyz,f_xyz,v_xyz, mme ); ++ ++if(mytaskid=3D=3D0) ++ printf( "md returns %d\n", ier ); +diff -urN amber11.orig/AmberTools/test/nab/rismion.out.check amber11/Amb= erTools/test/nab/rismion.out.check +--- amber11.orig/AmberTools/test/nab/rismion.out.check 1970-01-01 03:00:= 00.000000000 +0300 ++++ amber11/AmberTools/test/nab/rismion.out.check 2011-03-08 16:38:44.00= 0000000 +0300 +@@ -0,0 +1,24 @@ ++Reading parm file (Na+.parm7) ++title: ++ = =20 ++ mm_options: e_debug=3D0 ++ mm_options: ntpr=3D1 ++ mm_options: ntpr_md=3D1 ++ mm_options: cut=3D999.0 ++ mm_options: dt=3D0.001 ++ mm_options: rattle=3D0 ++ mm_options: tempi=3D0 ++ mm_options: zerov=3D0 ++ mm_options: rism=3D1 ++ mm_options: apply_rism_force=3D0 ++ mm_options: buffer=3D12 ++ mm_options: solvcut=3D999 ++ mm_options: progress=3D1 ++ mm_options: xvvfile=3D../rism1d/spc/spc-nacl.xvv.save ++| New format PARM file being parsed. ++| Version =3D 0.001 Date =3D 04:06:10 Time =3D 16:41:39 ++ iter Total bad vdW elect nonpolar genBorn = frms ++ nblist_box, number of atoms=3D 1 ++ nblist_box, number of pairs=3D 0 ++ff: 0 -73.97 0.00 0.00 0.00 0.00 -73.97 = 0.00e+00 ++md returns 0 +diff -urN amber11.orig/AmberTools/test/nab/Run.rism_ion amber11/AmberToo= ls/test/nab/Run.rism_ion +--- amber11.orig/AmberTools/test/nab/Run.rism_ion 1970-01-01 03:00:00.00= 0000000 +0300 ++++ amber11/AmberTools/test/nab/Run.rism_ion 2011-03-08 16:38:44.0000000= 00 +0300 +@@ -0,0 +1,39 @@ ++#!/bin/sh ++ ++toomany() { ++ echo "${0}: This test requires 1, 2, 3, 4, 6, 8, 12 or 24 processes= " ++ echo "for meaningful comparison." ++ exit 0 ++} ++ ++if [ -n "${DO_PARALLEL}" ] ; then ++ numprocs=3D`echo $DO_PARALLEL | awk -f ../numprocs.awk ` ++ if [ ! \( "$numprocs" -eq "12" -o "$numprocs" -eq "24"\ ++ -o "$numprocs" -eq "8" -o "$numprocs" -eq "6"\ ++ -o "$numprocs" -eq "3" -o "$numprocs" -eq "4"\ ++ -o "$numprocs" -eq "2" -o "$numprocs" -le "1" \) ]; then ++ echo " DO_PARALLEL set to $DO_PARALLEL" ++ toomany=20 ++ elif [ -n "${MP_PROCS}" ]; then ++ if [ ! \( "$MP_PROCS" -eq "12" -o "$MP_PROCS" -eq "24"\ ++ -o "$MP_PROCS" -eq "8" -o "$MP_PROCS" -eq "6"\ ++ -o "$MP_PROCS" -eq "3" -o "$MP_PROCS" -eq "4"\ ++ -o "$MP_PROCS" -eq "2" -o "$MP_PROCS" -le "1" \) ]; then ++# --- For IBM AIX --- ++ echo " MP_PROCS set to "$MP_PROCS ++ toomany=20 ++ fi ++ fi ++fi ++. ../program_error.sh ++ ++echo "Running test for ionic solvent and charge solute" ++echo "(this tests the 3D-RISM-KH implementation)" ++echo "" ++../../bin/nab -o sff rismion.nab || error ++$DO_PARALLEL ./sff > rismion.out || error ++ ++../dacdif rismion.out.check rismion.out ++ ++rm -f sff rismion.c ++exit 0 +diff -urN amber11.orig/AmberTools/test/sleap/glycam/n.pdb.save amber11/A= mberTools/test/sleap/glycam/n.pdb.save +--- amber11.orig/AmberTools/test/sleap/glycam/n.pdb.save 2010-03-31 07:0= 5:23.000000000 +0400 ++++ amber11/AmberTools/test/sleap/glycam/n.pdb.save 2011-03-08 16:38:44.= 000000000 +0300 +@@ -8,13 +8,13 @@ + ATOM 8 O4 6LB 1 5.435 3.303 2.147 1.00 0.00 + ATOM 9 H4O 6LB 1 5.122 4.155 1.839 1.00 0.00 + ATOM 10 C3 6LB 1 5.271 3.073 -0.262 1.00 0.00 +-ATOM 11 H3 6LB 1 4.894 2.740 -1.242 1.00 0.00 +-ATOM 12 O3 6LB 1 6.571 3.630 -0.399 1.00 0.00 +-ATOM 13 H3O 6LB 1 7.188 2.917 -0.649 1.00 0.00 +-ATOM 14 C2 6LB 1 4.314 4.119 0.310 1.00 0.00 +-ATOM 15 H2 6LB 1 3.733 4.482 1.177 1.00 0.00 +-ATOM 16 O2 6LB 1 5.419 4.938 -0.016 1.00 0.00 +-ATOM 17 H2O 6LB 1 6.213 5.114 -0.520 1.00 0.00 ++ATOM 11 H3 6LB 1 5.706 2.518 -1.108 1.00 0.00 ++ATOM 12 O3 6LB 1 5.591 4.453 -0.363 1.00 0.00 ++ATOM 13 H3O 6LB 1 6.553 4.558 -0.232 1.00 0.00 ++ATOM 14 C2 6LB 1 3.753 2.890 -0.273 1.00 0.00 ++ATOM 15 H2 6LB 1 3.395 3.508 0.570 1.00 0.00 ++ATOM 16 O2 6LB 1 3.239 3.287 -1.528 1.00 0.00 ++ATOM 17 H2O 6LB 1 2.352 3.631 -1.425 1.00 0.00 + ATOM 18 C6 6LB 1 5.842 0.516 2.583 1.00 0.00 + ATOM 19 H61 6LB 1 6.928 0.603 2.654 1.00 0.00 + ATOM 20 H62 6LB 1 5.375 1.096 3.383 1.00 0.00 +@@ -37,7 +37,7 @@ + ATOM 37 C2 VLB 2 4.686 -2.097 4.639 1.00 0.00 + ATOM 38 H2 VLB 2 4.209 -2.878 4.019 1.00 0.00 + ATOM 39 O2 VLB 2 3.816 -1.039 4.992 1.00 0.00 +-ATOM 40 H2O VLB 2 2.957 -1.387 4.762 1.00 0.00 ++ATOM 40 H2O VLB 2 4.332 -0.238 5.050 1.00 0.00 + ATOM 41 O3 VLB 2 4.014 -3.472 6.508 1.00 0.00 + ATOM 42 C1 VLB 3 2.893 -2.701 6.920 1.00 0.00 + ATOM 43 H1 VLB 3 3.071 -1.648 6.648 1.00 0.00 +@@ -57,7 +57,7 @@ + ATOM 57 C2 VLB 3 1.614 -3.056 6.171 1.00 0.00 + ATOM 58 H2 VLB 3 1.323 -4.090 6.432 1.00 0.00 + ATOM 59 O2 VLB 3 1.793 -2.849 4.782 1.00 0.00 +-ATOM 60 H2O VLB 3 1.405 -3.634 4.401 1.00 0.00 ++ATOM 60 H2O VLB 3 2.476 -2.193 4.666 1.00 0.00 + ATOM 61 O3 VLB 3 -0.763 -2.638 6.079 1.00 0.00 + ATOM 62 C1 3GB 4 -0.905 -2.644 4.665 1.00 0.00 + ATOM 63 H1 3GB 4 0.044 -2.311 4.215 1.00 0.00 +@@ -68,7 +68,7 @@ + ATOM 68 H61 3GB 4 -3.380 -0.533 1.560 1.00 0.00 + ATOM 69 H62 3GB 4 -4.134 -1.031 3.099 1.00 0.00 + ATOM 70 O6 3GB 4 -2.909 0.649 3.114 1.00 0.00 +-ATOM 71 H6O 3GB 4 -3.688 0.628 3.666 1.00 0.00 ++ATOM 71 H6O 3GB 4 -2.709 0.580 4.045 1.00 0.00 + ATOM 72 C4 3GB 4 -2.352 -2.990 2.187 1.00 0.00 + ATOM 73 H4 3GB 4 -3.330 -3.384 2.501 1.00 0.00 + ATOM 74 O4 3GB 4 -2.343 -2.789 0.771 1.00 0.00 +@@ -78,7 +78,7 @@ + ATOM 78 C2 3GB 4 -1.106 -4.042 4.090 1.00 0.00 + ATOM 79 H2 3GB 4 -2.075 -4.437 4.446 1.00 0.00 + ATOM 80 O2 3GB 4 -0.002 -4.864 4.416 1.00 0.00 +-ATOM 81 H2O 3GB 4 0.874 -5.115 4.125 1.00 0.00 ++ATOM 81 H2O 3GB 4 -0.154 -5.298 5.256 1.00 0.00 + ATOM 82 O3 3GB 4 -1.600 -5.254 2.060 1.00 0.00 + ATOM 83 C1 0GB 5 -0.735 -6.360 2.282 1.00 0.00 + ATOM 84 H1 0GB 5 0.116 -6.024 2.897 1.00 0.00 +@@ -89,7 +89,7 @@ + ATOM 89 H61 0GB 5 1.836 -9.117 -0.171 1.00 0.00 + ATOM 90 H62 0GB 5 0.236 -8.623 -0.788 1.00 0.00 + ATOM 91 O6 0GB 5 1.789 -7.246 -0.898 1.00 0.00 +-ATOM 92 H6O 0GB 5 1.142 -7.286 -1.600 1.00 0.00 ++ATOM 92 H6O 0GB 5 1.207 -6.488 -0.919 1.00 0.00 + ATOM 93 C4 0GB 5 0.134 -9.099 1.971 1.00 0.00 + ATOM 94 H4 0GB 5 -0.679 -9.576 1.404 1.00 0.00 + ATOM 95 O4 0GB 5 1.193 -10.038 2.180 1.00 0.00 +@@ -103,49 +103,49 @@ + ATOM 103 O2 0GB 5 -1.753 -6.949 4.385 1.00 0.00 + ATOM 104 H2O 0GB 5 -2.644 -6.603 4.344 1.00 0.00 + TER +-ATOM 105 C1 3LB 6 10.501 -4.485 3.172 1.00 0.00 +-ATOM 106 H1 3LB 6 10.220 -5.544 3.293 1.00 0.00 +-ATOM 107 O5 3LB 6 11.709 -4.218 3.853 1.00 0.00 +-ATOM 108 C5 3LB 6 12.798 -5.075 3.481 1.00 0.00 +-ATOM 109 H5 3LB 6 12.529 -6.122 3.711 1.00 0.00 +-ATOM 110 C6 3LB 6 13.974 -4.687 4.358 1.00 0.00 +-ATOM 111 H61 3LB 6 14.831 -5.300 4.073 1.00 0.00 +-ATOM 112 H62 3LB 6 14.206 -3.632 4.190 1.00 0.00 +-ATOM 113 O6 3LB 6 13.745 -4.955 5.727 1.00 0.00 +-ATOM 114 H6O 3LB 6 13.914 -4.037 5.928 1.00 0.00 +-ATOM 115 C4 3LB 6 13.095 -4.959 1.987 1.00 0.00 +-ATOM 116 H4 3LB 6 13.857 -5.698 1.700 1.00 0.00 +-ATOM 117 O4 3LB 6 13.583 -3.638 1.737 1.00 0.00 +-ATOM 118 H4O 3LB 6 13.207 -3.313 0.918 1.00 0.00 +-ATOM 119 C3 3LB 6 11.834 -5.224 1.182 1.00 0.00 +-ATOM 120 H3 3LB 6 11.550 -6.279 1.318 1.00 0.00 +-ATOM 121 C2 3LB 6 10.690 -4.332 1.666 1.00 0.00 +-ATOM 122 H2 3LB 6 11.034 -3.304 1.454 1.00 0.00 +-ATOM 123 O2 3LB 6 9.498 -4.685 0.991 1.00 0.00 +-ATOM 124 H2O 3LB 6 9.019 -5.430 0.628 1.00 0.00 +-ATOM 125 O3 3LB 6 12.104 -4.961 -0.188 1.00 0.00 +-ATOM 126 C1 0GB 7 11.081 -5.133 -1.159 1.00 0.00 +-ATOM 127 H1 0GB 7 10.154 -5.434 -0.645 1.00 0.00 +-ATOM 128 O5 0GB 7 11.461 -6.115 -2.101 1.00 0.00 +-ATOM 129 C5 0GB 7 10.440 -6.444 -3.054 1.00 0.00 +-ATOM 130 H5 0GB 7 9.559 -6.842 -2.518 1.00 0.00 +-ATOM 131 C6 0GB 7 11.002 -7.552 -3.925 1.00 0.00 +-ATOM 132 H61 0GB 7 10.258 -7.800 -4.686 1.00 0.00 +-ATOM 133 H62 0GB 7 11.913 -7.191 -4.409 1.00 0.00 +-ATOM 134 O6 0GB 7 11.234 -8.746 -3.207 1.00 0.00 +-ATOM 135 H6O 0GB 7 12.148 -8.727 -3.483 1.00 0.00 +-ATOM 136 C4 0GB 7 10.017 -5.207 -3.846 1.00 0.00 +-ATOM 137 H4 0GB 7 10.852 -4.864 -4.475 1.00 0.00 +-ATOM 138 O4 0GB 7 8.908 -5.572 -4.672 1.00 0.00 +-ATOM 139 H4O 0GB 7 9.006 -5.159 -5.530 1.00 0.00 +-ATOM 140 C3 0GB 7 9.603 -4.096 -2.897 1.00 0.00 +-ATOM 141 H3 0GB 7 8.685 -4.408 -2.376 1.00 0.00 +-ATOM 142 O3 0GB 7 9.362 -2.917 -3.653 1.00 0.00 +-ATOM 143 H3O 0GB 7 8.751 -3.136 -4.381 1.00 0.00 +-ATOM 144 C2 0GB 7 10.699 -3.835 -1.863 1.00 0.00 +-ATOM 145 H2 0GB 7 11.561 -3.486 -2.459 1.00 0.00 +-ATOM 146 O2 0GB 7 10.240 -2.889 -0.917 1.00 0.00 +-ATOM 147 H2O 0GB 7 10.975 -2.374 -0.585 1.00 0.00 ++ATOM 105 C1 3LB 6 3.394 1.433 0.000 1.00 0.00 ++ATOM 106 H1 3LB 6 3.836 0.891 -0.851 1.00 0.00 ++ATOM 107 O5 3LB 6 3.973 0.998 1.212 1.00 0.00 ++ATOM 108 C5 3LB 6 5.405 1.087 1.247 1.00 0.00 ++ATOM 109 H5 3LB 6 5.826 0.451 0.448 1.00 0.00 ++ATOM 110 C6 3LB 6 5.842 0.516 2.583 1.00 0.00 ++ATOM 111 H61 3LB 6 6.928 0.603 2.654 1.00 0.00 ++ATOM 112 H62 3LB 6 5.375 1.096 3.383 1.00 0.00 ++ATOM 113 O6 3LB 6 5.555 -0.862 2.707 1.00 0.00 ++ATOM 114 H6O 3LB 6 4.615 -0.981 2.592 1.00 0.00 ++ATOM 115 C4 3LB 6 5.865 2.527 1.025 1.00 0.00 ++ATOM 116 H4 3LB 6 6.962 2.560 0.948 1.00 0.00 ++ATOM 117 O4 3LB 6 5.435 3.303 2.147 1.00 0.00 ++ATOM 118 H4O 3LB 6 5.122 4.155 1.839 1.00 0.00 ++ATOM 119 C3 3LB 6 5.271 3.073 -0.262 1.00 0.00 ++ATOM 120 H3 3LB 6 5.706 2.518 -1.108 1.00 0.00 ++ATOM 121 C2 3LB 6 3.753 2.890 -0.273 1.00 0.00 ++ATOM 122 H2 3LB 6 3.395 3.508 0.570 1.00 0.00 ++ATOM 123 O2 3LB 6 3.238 3.288 -1.530 1.00 0.00 ++ATOM 124 H2O 3LB 6 2.351 3.631 -1.427 1.00 0.00 ++ATOM 125 O3 3LB 6 5.591 4.453 -0.363 1.00 0.00 ++ATOM 126 C1 0GB 7 5.149 5.205 -1.484 1.00 0.00 ++ATOM 127 H1 0GB 7 4.548 4.549 -2.133 1.00 0.00 ++ATOM 128 O5 0GB 7 6.255 5.718 -2.197 1.00 0.00 ++ATOM 129 C5 0GB 7 5.911 6.393 -3.416 1.00 0.00 ++ATOM 130 H5 0GB 7 5.402 5.682 -4.091 1.00 0.00 ++ATOM 131 C6 0GB 7 7.218 6.805 -4.066 1.00 0.00 ++ATOM 132 H61 0GB 7 6.987 7.354 -4.981 1.00 0.00 ++ATOM 133 H62 0GB 7 7.764 7.455 -3.378 1.00 0.00 ++ATOM 134 O6 0GB 7 8.002 5.699 -4.466 1.00 0.00 ++ATOM 135 H6O 0GB 7 8.174 5.164 -3.694 1.00 0.00 ++ATOM 136 C4 0GB 7 4.976 7.569 -3.140 1.00 0.00 ++ATOM 137 H4 0GB 7 5.507 8.340 -2.562 1.00 0.00 ++ATOM 138 O4 0GB 7 4.562 8.106 -4.399 1.00 0.00 ++ATOM 139 H4O 0GB 7 4.551 9.062 -4.345 1.00 0.00 ++ATOM 140 C3 0GB 7 3.759 7.096 -2.362 1.00 0.00 ++ATOM 141 H3 0GB 7 3.169 6.430 -3.010 1.00 0.00 ++ATOM 142 O3 0GB 7 2.987 8.230 -1.991 1.00 0.00 ++ATOM 143 H3O 0GB 7 2.828 8.771 -2.788 1.00 0.00 ++ATOM 144 C2 0GB 7 4.185 6.326 -1.112 1.00 0.00 ++ATOM 145 H2 0GB 7 4.726 7.072 -0.501 1.00 0.00 ++ATOM 146 O2 0GB 7 3.042 5.790 -0.474 1.00 0.00 ++ATOM 147 H2O 0GB 7 3.187 5.738 0.470 1.00 0.00 + CONECT 1 2 3 14 + CONECT 2 1 + CONECT 3 1 4 +@@ -173,7 +173,7 @@ + CONECT 25 24 26 27 31 + CONECT 26 25 + CONECT 27 25 28 29 30 +-CONECT 28 27 105 ++CONECT 28 27 + CONECT 29 27 + CONECT 30 27 + CONECT 31 25 32 33 35 +@@ -250,7 +250,7 @@ + CONECT 102 101 + CONECT 103 101 104 + CONECT 104 103 +-CONECT 105 28 106 107 121 ++CONECT 105 106 107 121 + CONECT 106 105 + CONECT 107 105 108 + CONECT 108 107 109 110 115 +diff -urN amber11.orig/AmberTools/test/sleap/oldleap/ff91/all_amino91.li= b.save amber11/AmberTools/test/sleap/oldleap/ff91/all_amino91.lib.save +--- amber11.orig/AmberTools/test/sleap/oldleap/ff91/all_amino91.lib.save= 2010-03-31 07:05:23.000000000 +0400 ++++ amber11/AmberTools/test/sleap/oldleap/ff91/all_amino91.lib.save 2011= -03-08 16:38:44.000000000 +0300 +@@ -256,7 +256,7 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.230747 4.925147 1.196914 +- 4.828085 5.500165 0.713033 ++ 3.983296 5.433818 1.972557 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.SER.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -368,7 +368,7 @@ + 1.784422 4.436955 2.124895 + 1.764698 4.397850 0.345787 + 3.971494 2.947416 2.411212 +- 4.374397 3.770738 2.696536 ++ 3.724043 3.456087 3.186855 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.THR.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -500,15 +500,15 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.857033 4.748192 2.579338 +- 5.821217 4.249596 2.480083 +- 4.990360 5.695010 3.102655 +- 4.176711 4.112860 3.146449 +- 5.226485 5.898474 0.401698 +- 5.794506 5.938748 1.331123 +- 5.883342 6.134649 -0.435476 +- 4.414018 6.624028 0.441300 ++ 5.354265 4.863179 1.185791 ++ 3.853427 5.762894 -0.062862 ++ 2.773446 5.910110 -0.054565 ++ 4.351509 6.732051 -0.090207 ++ 4.134162 5.185701 -0.943848 ++ 3.881095 5.817649 2.426715 ++ 4.181612 5.279606 3.325770 ++ 4.379188 6.786828 2.400358 ++ 2.801124 5.964886 2.435947 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.LEU.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -648,12 +648,12 @@ + 3.671552 3.399212 3.380613 + 3.485641 1.869279 2.490736 + 4.230199 4.986696 1.245167 +- 3.258221 5.469711 1.345449 +- 4.638709 4.784431 2.235272 +- 5.178160 5.906245 0.482655 +- 5.735477 5.933935 1.418994 +- 5.840562 6.170139 -0.341774 +- 4.354989 6.619215 0.529171 ++ 5.312304 4.855747 1.245167 ++ 3.931816 5.541027 0.355344 ++ 3.812283 5.761636 2.490333 ++ 4.110763 5.208108 3.380624 ++ 4.296680 6.738088 2.490828 ++ 2.730275 5.893388 2.490801 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.ILE.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -781,9 +781,9 @@ + 3.716963 3.477633 3.370556 + 3.499621 1.931327 2.516833 + 4.274181 5.009604 1.194574 +- 4.690774 4.823320 2.184447 +- 4.954792 5.645336 0.628258 +- 3.310286 5.508600 1.294624 ++ 3.973778 5.548459 0.295968 ++ 3.993550 5.587589 2.075074 ++ 5.354265 4.863179 1.185791 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.VAL.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -897,10 +897,10 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.253694 5.017114 1.232141 +- 3.666601 5.213107 2.293908 +- 5.062354 5.920372 0.673198 +- 5.699537 6.377296 0.036552 +- 4.754312 6.389897 1.512695 ++ 5.005295 5.340406 0.315070 ++ 3.984875 5.817912 2.265912 ++ 4.408006 6.733705 2.314738 ++ 3.359598 5.504301 2.994456 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.ASN.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -1024,13 +1024,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.220277 5.927344 0.433563 +- 4.913588 6.591689 1.420998 +- 6.050965 6.373808 -0.511346 +- 5.971268 7.107959 0.177690 +- 6.636748 6.497679 -1.324743 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.906966 5.848446 2.410297 ++ 3.138947 5.408353 3.262885 ++ 4.458847 7.061526 2.488328 ++ 4.248421 7.659050 3.274958 ++ 5.084275 7.376210 1.760376 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.GLN.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -1185,20 +1185,20 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.226485 5.898474 0.401698 +- 4.414018 6.624028 0.441300 +- 5.794506 5.938748 1.331123 +- 6.125319 6.253797 -0.719124 +- 6.688164 6.300372 -1.556463 +- 6.117846 7.301883 0.099632 +- 5.907135 8.163840 1.090353 +- 5.292210 7.913283 1.851398 +- 6.363014 9.065005 1.077109 +- 6.926823 7.627695 -0.904511 +- 7.501836 7.713669 -1.730386 +- 6.873063 8.384728 -0.238094 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.881095 5.817649 2.426715 ++ 2.801124 5.964886 2.435947 ++ 4.181612 5.279606 3.325770 ++ 4.540311 7.142726 2.424478 ++ 5.151800 7.375491 1.655062 ++ 4.364270 8.040994 3.389374 ++ 3.575005 7.807613 4.434120 ++ 3.088928 6.925430 4.508833 ++ 3.465343 8.513638 5.147984 ++ 5.006244 9.201290 3.286985 ++ 5.604850 9.375324 2.492326 ++ 4.892201 9.903050 4.004360 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.ARG.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -1333,13 +1333,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.003504 6.072258 0.881472 +- 4.722990 6.580423 1.708019 +- 5.824163 6.508104 -0.056055 +- 5.654216 7.217462 0.753902 +- 6.562760 6.595751 -1.134430 +- 7.210678 6.375009 -2.309622 +- 7.387392 7.342143 -1.838959 ++ 3.942772 5.885090 2.382967 ++ 3.339711 5.691917 3.169798 ++ 4.624266 6.997644 2.182496 ++ 4.563036 7.811879 2.904557 ++ 5.294008 6.891449 1.061662 ++ 5.058971 5.678865 0.492455 ++ 5.537740 5.417840 -0.451339 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.HID.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -1467,13 +1467,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.003504 6.072258 0.881472 +- 5.824163 6.508104 -0.056055 +- 5.654216 7.217462 0.753902 +- 6.562760 6.595751 -1.134430 +- 6.629203 7.441424 -0.586231 +- 7.210678 6.375009 -2.309622 +- 7.387392 7.342143 -1.838959 ++ 3.942772 5.885090 2.382967 ++ 4.624266 6.997644 2.182496 ++ 4.563036 7.811879 2.904557 ++ 5.294008 6.891449 1.061662 ++ 5.896295 7.605082 0.676854 ++ 5.058971 5.678865 0.492455 ++ 5.537740 5.417840 -0.451339 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.HIE.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -1605,14 +1605,14 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.003504 6.072258 0.881472 +- 4.722990 6.580423 1.708019 +- 5.824163 6.508104 -0.056055 +- 5.654216 7.217462 0.753902 +- 6.562760 6.595751 -1.134430 +- 6.629203 7.441424 -0.586231 +- 7.210678 6.375009 -2.309622 +- 7.387392 7.342143 -1.838959 ++ 3.942772 5.885090 2.382967 ++ 3.339711 5.691917 3.169798 ++ 4.624266 6.997644 2.182496 ++ 4.563036 7.811879 2.904557 ++ 5.294008 6.891449 1.061662 ++ 5.896295 7.605082 0.676854 ++ 5.058971 5.678865 0.492455 ++ 5.537740 5.417840 -0.451339 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.HIP.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -1770,20 +1770,20 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 4.941957 6.093161 0.993054 +- 4.555798 6.518222 1.919501 +- 5.833674 6.587638 -0.009560 +- 5.727864 7.297382 0.701192 +- 6.577083 6.691104 -1.083216 +- 6.699953 7.881667 -0.356949 +- 7.350710 8.089828 -1.206234 +- 6.471604 8.773711 0.684306 +- 7.153163 9.167983 -0.069436 +- 6.163215 9.539474 1.752484 +- 6.850900 10.076243 1.098979 +- 5.726463 10.185215 2.927374 +- 6.404130 10.841773 2.381664 +- 5.125146 10.546906 4.138818 ++ 4.023443 5.931088 2.293236 ++ 3.368827 5.705470 3.135064 ++ 4.811936 7.073557 1.949805 ++ 4.882911 7.922013 2.493114 ++ 5.427345 6.842058 0.816764 ++ 6.297161 7.689048 0.119607 ++ 6.531228 8.676646 0.517052 ++ 6.814097 7.187003 -1.069017 ++ 7.498083 7.791848 -1.664355 ++ 6.482667 5.953109 -1.505090 ++ 6.897672 5.575635 -2.439640 ++ 5.604046 5.117349 -0.785625 ++ 5.358725 4.126563 -1.168065 ++ 5.083391 5.623006 0.411551 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.TRP.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -1930,16 +1930,16 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.021223 6.053049 0.839188 +- 4.662984 6.521610 1.755820 +- 5.904492 6.742286 -0.000329 +- 5.724114 7.440373 0.817130 +- 6.758713 7.099630 -1.050381 +- 6.738282 7.947511 -0.365705 +- 7.536653 7.157250 -2.212917 +- 7.655187 8.096815 -1.673224 +- 8.214242 6.953605 -3.420974 +- 8.451251 7.942064 -3.027432 ++ 3.911603 5.857254 2.409885 ++ 3.236109 5.513847 3.193390 ++ 4.490005 7.129516 2.492349 ++ 4.264839 7.776656 3.340058 ++ 5.357612 7.570590 1.486013 ++ 5.807939 8.561136 1.550217 ++ 5.646816 6.739401 0.397212 ++ 6.322310 7.082808 -0.386292 ++ 5.068414 5.467139 0.314748 ++ 5.293580 4.820000 -0.532961 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.PHE.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -2086,17 +2086,17 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.267323 4.996269 1.194944 +- 5.102503 5.984523 0.660315 +- 4.777863 6.502414 1.562811 +- 5.985574 6.611197 -0.227077 +- 5.846174 7.352316 0.559949 +- 6.824378 6.891857 -1.312267 +- 6.854321 7.991157 -0.512116 +- 6.305234 7.900783 0.270147 +- 7.573657 6.866032 -2.494602 +- 7.737299 7.827553 -2.007982 +- 8.211756 6.577405 -3.706841 +- 8.492629 7.576371 -3.373257 ++ 4.059917 5.918914 2.227275 ++ 3.400094 5.668222 3.057870 ++ 4.699989 7.163550 2.192787 ++ 4.538509 7.881896 2.996531 ++ 5.547468 7.485540 1.125968 ++ 6.169252 8.694615 1.092466 ++ 5.956320 9.246984 1.848209 ++ 5.754874 6.562895 0.093637 ++ 6.414696 6.813587 -0.736958 ++ 5.114801 5.318259 0.128125 ++ 5.276282 4.599913 -0.675619 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.TYR.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -2219,11 +2219,11 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.267323 4.996269 1.194944 +- 3.302423 5.493308 1.295046 +- 4.682911 4.808028 2.184869 +- 5.220383 5.890117 0.404729 +- 6.306867 5.987364 1.035359 +- 4.568248 6.850423 -0.085305 ++ 5.347407 4.849844 1.186161 ++ 3.966920 5.535124 0.296338 ++ 3.873721 5.805373 2.428701 ++ 4.594575 5.679017 3.454373 ++ 2.855955 6.542075 2.333709 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.GLU.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -2328,8 +2328,8 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.275095 5.011382 1.194525 +- 5.214909 5.080371 2.030940 +- 3.476290 5.943429 0.910275 ++ 3.669104 5.954940 0.620005 ++ 5.407723 5.091882 1.740669 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.ASP.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -2471,18 +2471,18 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.226485 5.898474 0.401698 +- 4.414018 6.624028 0.441300 +- 5.794506 5.938748 1.331123 +- 6.145332 6.228186 -0.769897 +- 7.203874 5.974714 -0.827698 +- 5.823386 6.659994 -1.717522 +- 5.933539 7.203239 0.309601 +- 6.482814 7.265694 1.154880 +- 6.528435 7.362078 -0.491005 +- 5.203409 7.900796 0.330212 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.881095 5.817649 2.426715 ++ 2.801124 5.964886 2.435947 ++ 4.181612 5.279606 3.325770 ++ 4.578316 7.173413 2.389148 ++ 5.658401 7.026988 2.380365 ++ 4.277913 7.712268 1.490542 ++ 4.199407 7.952315 3.576852 ++ 4.478064 7.453372 4.409622 ++ 4.661173 8.850231 3.551971 ++ 3.198660 8.088474 3.584954 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.LYS.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -2600,11 +2600,11 @@ + 4.419995 0.019280 -0.902255 + 3.955884 -0.274036 0.790585 + 5.547124 1.172442 0.544698 +- 6.078592 2.122578 0.598404 +- 6.005141 0.543154 -0.218399 +- 5.532142 0.472642 1.882665 +- 6.368845 0.104645 1.288859 +- 5.876555 1.272377 2.538335 ++ 6.413547 0.741633 0.042886 ++ 5.652946 1.047940 1.622381 ++ 5.369090 2.628183 0.185221 ++ 5.690639 3.251042 1.019939 ++ 5.969291 2.861853 -0.694128 + 3.933608 2.871277 -0.104508 + 3.932642 3.351380 0.874062 + 2.872953 3.958248 -0.204456 +@@ -2714,9 +2714,9 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.309567 5.303525 1.366033 +- 5.145787 5.839753 0.481671 +- 4.563172 5.041444 1.938780 +- 3.657120 5.491212 1.354764 ++ 3.725381 5.622023 2.517634 ++ 4.051868 5.551722 0.788945 ++ 4.957920 5.101954 1.372960 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.CYS.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -2819,8 +2819,8 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.309567 5.303525 1.366033 +- 4.563172 5.041444 1.938780 +- 3.657120 5.491212 1.354764 ++ 4.051868 5.551722 0.788945 ++ 4.957920 5.101954 1.372960 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.CYX.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -2950,15 +2950,15 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.402881 6.076526 0.265157 +- 5.724538 5.972445 0.854008 +- 4.818486 6.422214 0.269993 +- 6.377314 6.105674 -1.224148 +- 6.034578 6.467191 -2.193651 +- 6.303017 6.908485 -0.490613 +- 7.415066 5.781911 -1.303828 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.817297 5.981271 2.651702 ++ 4.055297 5.545795 3.115122 ++ 3.149245 5.995564 2.531107 ++ 4.753204 7.463130 2.340945 ++ 4.433578 7.904044 1.396734 ++ 4.585895 8.175303 3.148978 ++ 5.814065 7.218764 2.286557 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.MET.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +diff -urN amber11.orig/AmberTools/test/sleap/oldleap/ff91/all_aminoct91.= lib.save amber11/AmberTools/test/sleap/oldleap/ff91/all_aminoct91.lib.sav= e +--- amber11.orig/AmberTools/test/sleap/oldleap/ff91/all_aminoct91.lib.sa= ve 2010-03-31 07:05:23.000000000 +0400 ++++ amber11/AmberTools/test/sleap/oldleap/ff91/all_aminoct91.lib.save 20= 11-03-08 16:38:44.000000000 +0300 +@@ -272,7 +272,7 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.230747 4.925147 1.196914 +- 4.828085 5.500165 0.713033 ++ 3.983296 5.433818 1.972557 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -390,7 +390,7 @@ + 1.784422 4.436955 2.124895 + 1.764698 4.397850 0.345787 + 3.971494 2.947416 2.411212 +- 4.374397 3.770738 2.696536 ++ 3.724043 3.456087 3.186855 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -528,15 +528,15 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.857033 4.748192 2.579338 +- 5.821217 4.249596 2.480083 +- 4.990360 5.695010 3.102655 +- 4.176711 4.112860 3.146449 +- 5.226485 5.898474 0.401698 +- 5.794506 5.938748 1.331123 +- 5.883342 6.134649 -0.435476 +- 4.414018 6.624028 0.441300 ++ 5.354265 4.863179 1.185791 ++ 3.853427 5.762894 -0.062862 ++ 2.773446 5.910110 -0.054565 ++ 4.351509 6.732051 -0.090207 ++ 4.134162 5.185701 -0.943848 ++ 3.881095 5.817649 2.426715 ++ 4.181612 5.279606 3.325770 ++ 4.379188 6.786828 2.400358 ++ 2.801124 5.964886 2.435947 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -682,12 +682,12 @@ + 3.671552 3.399212 3.380613 + 3.485641 1.869279 2.490736 + 4.230199 4.986696 1.245167 +- 3.258221 5.469711 1.345449 +- 4.638709 4.784431 2.235272 +- 5.178160 5.906245 0.482655 +- 5.735477 5.933935 1.418994 +- 5.840562 6.170139 -0.341774 +- 4.354989 6.619215 0.529171 ++ 5.312304 4.855747 1.245167 ++ 3.931816 5.541027 0.355344 ++ 3.812283 5.761636 2.490333 ++ 4.110763 5.208108 3.380624 ++ 4.296680 6.738088 2.490828 ++ 2.730275 5.893388 2.490801 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -821,9 +821,9 @@ + 3.716963 3.477633 3.370556 + 3.499621 1.931327 2.516833 + 4.274181 5.009604 1.194574 +- 4.690774 4.823320 2.184447 +- 4.954792 5.645336 0.628258 +- 3.310286 5.508600 1.294624 ++ 3.973778 5.548459 0.295968 ++ 3.993550 5.587589 2.075074 ++ 5.354265 4.863179 1.185791 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -943,10 +943,10 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.253694 5.017114 1.232141 +- 3.666601 5.213107 2.293908 +- 5.062354 5.920372 0.673198 +- 5.699537 6.377296 0.036552 +- 4.754312 6.389897 1.512695 ++ 5.005295 5.340406 0.315070 ++ 3.984875 5.817912 2.265912 ++ 4.408006 6.733705 2.314738 ++ 3.359598 5.504301 2.994456 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -1076,13 +1076,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.220277 5.927344 0.433563 +- 4.913588 6.591689 1.420998 +- 6.050965 6.373808 -0.511346 +- 5.971268 7.107959 0.177690 +- 6.636748 6.497679 -1.324743 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.906966 5.848446 2.410297 ++ 3.138947 5.408353 3.262885 ++ 4.458847 7.061526 2.488328 ++ 4.248421 7.659050 3.274958 ++ 5.084275 7.376210 1.760376 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -1243,20 +1243,20 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.226485 5.898474 0.401698 +- 4.414018 6.624028 0.441300 +- 5.794506 5.938748 1.331123 +- 6.125319 6.253797 -0.719124 +- 6.688164 6.300372 -1.556463 +- 6.117846 7.301883 0.099632 +- 5.907135 8.163840 1.090353 +- 5.292210 7.913283 1.851398 +- 6.363014 9.065005 1.077109 +- 6.926823 7.627695 -0.904511 +- 7.501836 7.713669 -1.730386 +- 6.873063 8.384728 -0.238094 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.881095 5.817649 2.426715 ++ 2.801124 5.964886 2.435947 ++ 4.181612 5.279606 3.325770 ++ 4.540311 7.142726 2.424478 ++ 5.151800 7.375491 1.655062 ++ 4.364270 8.040994 3.389374 ++ 3.575005 7.807613 4.434120 ++ 3.088928 6.925430 4.508833 ++ 3.465343 8.513638 5.147984 ++ 5.006244 9.201290 3.286985 ++ 5.604850 9.375324 2.492326 ++ 4.892201 9.903050 4.004360 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -1397,13 +1397,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.003504 6.072258 0.881472 +- 4.722990 6.580423 1.708019 +- 5.824163 6.508104 -0.056055 +- 5.654216 7.217462 0.753902 +- 6.562760 6.595751 -1.134430 +- 7.210678 6.375009 -2.309622 +- 7.387392 7.342143 -1.838959 ++ 3.942772 5.885090 2.382967 ++ 3.339711 5.691917 3.169798 ++ 4.624266 6.997644 2.182496 ++ 4.563036 7.811879 2.904557 ++ 5.294008 6.891449 1.061662 ++ 5.058971 5.678865 0.492455 ++ 5.537740 5.417840 -0.451339 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -1537,13 +1537,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.003504 6.072258 0.881472 +- 5.824163 6.508104 -0.056055 +- 5.654216 7.217462 0.753902 +- 6.562760 6.595751 -1.134430 +- 6.629203 7.441424 -0.586231 +- 7.210678 6.375009 -2.309622 +- 7.387392 7.342143 -1.838959 ++ 3.942772 5.885090 2.382967 ++ 4.624266 6.997644 2.182496 ++ 4.563036 7.811879 2.904557 ++ 5.294008 6.891449 1.061662 ++ 5.896295 7.605082 0.676854 ++ 5.058971 5.678865 0.492455 ++ 5.537740 5.417840 -0.451339 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -1681,14 +1681,14 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.003504 6.072258 0.881472 +- 4.722990 6.580423 1.708019 +- 5.824163 6.508104 -0.056055 +- 5.654216 7.217462 0.753902 +- 6.562760 6.595751 -1.134430 +- 6.629203 7.441424 -0.586231 +- 7.210678 6.375009 -2.309622 +- 7.387392 7.342143 -1.838959 ++ 3.942772 5.885090 2.382967 ++ 3.339711 5.691917 3.169798 ++ 4.624266 6.997644 2.182496 ++ 4.563036 7.811879 2.904557 ++ 5.294008 6.891449 1.061662 ++ 5.896295 7.605082 0.676854 ++ 5.058971 5.678865 0.492455 ++ 5.537740 5.417840 -0.451339 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -1852,20 +1852,20 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 4.941957 6.093161 0.993054 +- 4.555798 6.518222 1.919501 +- 5.833674 6.587638 -0.009560 +- 5.727864 7.297382 0.701192 +- 6.577083 6.691104 -1.083216 +- 6.699953 7.881667 -0.356949 +- 7.350710 8.089828 -1.206234 +- 6.471604 8.773711 0.684306 +- 7.153163 9.167983 -0.069436 +- 6.163215 9.539474 1.752484 +- 6.850900 10.076243 1.098979 +- 5.726463 10.185215 2.927374 +- 6.404130 10.841773 2.381664 +- 5.125146 10.546906 4.138818 ++ 4.023443 5.931088 2.293236 ++ 3.368827 5.705470 3.135064 ++ 4.811936 7.073557 1.949805 ++ 4.882911 7.922013 2.493114 ++ 5.427345 6.842058 0.816764 ++ 6.297161 7.689048 0.119607 ++ 6.531228 8.676646 0.517052 ++ 6.814097 7.187003 -1.069017 ++ 7.498083 7.791848 -1.664355 ++ 6.482667 5.953109 -1.505090 ++ 6.897672 5.575635 -2.439640 ++ 5.604046 5.117349 -0.785625 ++ 5.358725 4.126563 -1.168065 ++ 5.083391 5.623006 0.411551 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -2018,16 +2018,16 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.021223 6.053049 0.839188 +- 4.662984 6.521610 1.755820 +- 5.904492 6.742286 -0.000329 +- 5.724114 7.440373 0.817130 +- 6.758713 7.099630 -1.050381 +- 6.738282 7.947511 -0.365705 +- 7.536653 7.157250 -2.212917 +- 7.655187 8.096815 -1.673224 +- 8.214242 6.953605 -3.420974 +- 8.451251 7.942064 -3.027432 ++ 3.911603 5.857254 2.409885 ++ 3.236109 5.513847 3.193390 ++ 4.490005 7.129516 2.492349 ++ 4.264839 7.776656 3.340058 ++ 5.357612 7.570590 1.486013 ++ 5.807939 8.561136 1.550217 ++ 5.646816 6.739401 0.397212 ++ 6.322310 7.082808 -0.386292 ++ 5.068414 5.467139 0.314748 ++ 5.293580 4.820000 -0.532961 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -2180,17 +2180,17 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.267323 4.996269 1.194944 +- 5.102503 5.984523 0.660315 +- 4.777863 6.502414 1.562811 +- 5.985574 6.611197 -0.227077 +- 5.846174 7.352316 0.559949 +- 6.824378 6.891857 -1.312267 +- 6.854321 7.991157 -0.512116 +- 6.305234 7.900783 0.270147 +- 7.573657 6.866032 -2.494602 +- 7.737299 7.827553 -2.007982 +- 8.211756 6.577405 -3.706841 +- 8.492629 7.576371 -3.373257 ++ 4.059917 5.918914 2.227275 ++ 3.400094 5.668222 3.057870 ++ 4.699989 7.163550 2.192787 ++ 4.538509 7.881896 2.996531 ++ 5.547468 7.485540 1.125968 ++ 6.169252 8.694615 1.092466 ++ 5.956320 9.246984 1.848209 ++ 5.754874 6.562895 0.093637 ++ 6.414696 6.813587 -0.736958 ++ 5.114801 5.318259 0.128125 ++ 5.276282 4.599913 -0.675619 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -2319,11 +2319,11 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.267323 4.996269 1.194944 +- 3.302423 5.493308 1.295046 +- 4.682911 4.808028 2.184869 +- 5.220383 5.890117 0.404729 +- 6.306867 5.987364 1.035359 +- 4.568248 6.850423 -0.085305 ++ 5.347407 4.849844 1.186161 ++ 3.966920 5.535124 0.296338 ++ 3.873721 5.805373 2.428701 ++ 4.594575 5.679017 3.454373 ++ 2.855955 6.542075 2.333709 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -2434,8 +2434,8 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.275095 5.011382 1.194525 +- 5.214909 5.080371 2.030940 +- 3.476290 5.943429 0.910275 ++ 3.669104 5.954940 0.620005 ++ 5.407723 5.091882 1.740669 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -2583,18 +2583,18 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.226485 5.898474 0.401698 +- 4.414018 6.624028 0.441300 +- 5.794506 5.938748 1.331123 +- 6.145332 6.228186 -0.769897 +- 7.203874 5.974714 -0.827698 +- 5.823386 6.659994 -1.717522 +- 5.933539 7.203239 0.309601 +- 6.482814 7.265694 1.154880 +- 6.528435 7.362078 -0.491005 +- 5.203409 7.900796 0.330212 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.881095 5.817649 2.426715 ++ 2.801124 5.964886 2.435947 ++ 4.181612 5.279606 3.325770 ++ 4.578316 7.173413 2.389148 ++ 5.658401 7.026988 2.380365 ++ 4.277913 7.712268 1.490542 ++ 4.199407 7.952315 3.576852 ++ 4.478064 7.453372 4.409622 ++ 4.661173 8.850231 3.551971 ++ 3.198660 8.088474 3.584954 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -2718,11 +2718,11 @@ + 4.419995 0.019280 -0.902255 + 3.955884 -0.274036 0.790585 + 5.547124 1.172442 0.544698 +- 6.078592 2.122578 0.598404 +- 6.005141 0.543154 -0.218399 +- 5.532142 0.472642 1.882665 +- 6.368845 0.104645 1.288859 +- 5.876555 1.272377 2.538335 ++ 6.413547 0.741633 0.042886 ++ 5.652946 1.047940 1.622381 ++ 5.369090 2.628183 0.185221 ++ 5.690639 3.251042 1.019939 ++ 5.969291 2.861853 -0.694128 + 3.933608 2.871277 -0.104508 + 3.932642 3.351380 0.874062 + 2.872953 3.958248 -0.204456 +@@ -2838,9 +2838,9 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.309567 5.303525 1.366033 +- 5.145787 5.839753 0.481671 +- 4.563172 5.041444 1.938780 +- 3.657120 5.491212 1.354764 ++ 3.725381 5.622023 2.517634 ++ 4.051868 5.551722 0.788945 ++ 4.957920 5.101954 1.372960 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -2949,8 +2949,8 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.309567 5.303525 1.366033 +- 4.563172 5.041444 1.938780 +- 3.657120 5.491212 1.354764 ++ 4.051868 5.551722 0.788945 ++ 4.957920 5.101954 1.372960 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -3086,15 +3086,15 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.402881 6.076526 0.265157 +- 5.724538 5.972445 0.854008 +- 4.818486 6.422214 0.269993 +- 6.377314 6.105674 -1.224148 +- 6.034578 6.467191 -2.193651 +- 6.303017 6.908485 -0.490613 +- 7.415066 5.781911 -1.303828 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.817297 5.981271 2.651702 ++ 4.055297 5.545795 3.115122 ++ 3.149245 5.995564 2.531107 ++ 4.753204 7.463130 2.340945 ++ 4.433578 7.904044 1.396734 ++ 4.585895 8.175303 3.148978 ++ 5.814065 7.218764 2.286557 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +diff -urN amber11.orig/AmberTools/test/sleap/oldleap/ff91/all_aminont91.= lib.save amber11/AmberTools/test/sleap/oldleap/ff91/all_aminont91.lib.sav= e +--- amber11.orig/AmberTools/test/sleap/oldleap/ff91/all_aminont91.lib.sa= ve 2010-03-31 07:05:23.000000000 +0400 ++++ amber11/AmberTools/test/sleap/oldleap/ff91/all_aminont91.lib.save 20= 11-03-08 16:38:44.000000000 +0300 +@@ -290,7 +290,7 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.230747 4.925147 1.196914 +- 4.828085 5.500165 0.713033 ++ 3.983296 5.433818 1.972557 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NSER.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -414,7 +414,7 @@ + 1.784422 4.436955 2.124895 + 1.764698 4.397850 0.345787 + 3.971494 2.947416 2.411212 +- 4.374397 3.770738 2.696536 ++ 3.724043 3.456087 3.186855 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NTHR.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -558,15 +558,15 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.857033 4.748192 2.579338 +- 5.821217 4.249596 2.480083 +- 4.990360 5.695010 3.102655 +- 4.176711 4.112860 3.146449 +- 5.226485 5.898474 0.401698 +- 5.794506 5.938748 1.331123 +- 5.883342 6.134649 -0.435476 +- 4.414018 6.624028 0.441300 ++ 5.354265 4.863179 1.185791 ++ 3.853427 5.762894 -0.062862 ++ 2.773446 5.910110 -0.054565 ++ 4.351509 6.732051 -0.090207 ++ 4.134162 5.185701 -0.943848 ++ 3.881095 5.817649 2.426715 ++ 4.181612 5.279606 3.325770 ++ 4.379188 6.786828 2.400358 ++ 2.801124 5.964886 2.435947 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NLEU.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -718,12 +718,12 @@ + 3.671552 3.399212 3.380613 + 3.485641 1.869279 2.490736 + 4.230199 4.986696 1.245167 +- 4.638709 4.784431 2.235272 +- 3.258221 5.469711 1.345449 +- 5.178160 5.906245 0.482655 +- 5.735477 5.933935 1.418994 +- 5.840562 6.170139 -0.341774 +- 4.354989 6.619215 0.529171 ++ 3.931816 5.541027 0.355344 ++ 5.312304 4.855747 1.245167 ++ 3.812283 5.761636 2.490333 ++ 4.110763 5.208108 3.380624 ++ 4.296680 6.738088 2.490828 ++ 2.730275 5.893388 2.490801 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NILE.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -863,9 +863,9 @@ + 3.716963 3.477633 3.370556 + 3.499621 1.931327 2.516833 + 4.274181 5.009604 1.194574 +- 4.690774 4.823320 2.184447 +- 4.954792 5.645336 0.628258 +- 3.310286 5.508600 1.294624 ++ 3.973778 5.548459 0.295968 ++ 3.993550 5.587589 2.075074 ++ 5.354265 4.863179 1.185791 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NVAL.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -991,10 +991,10 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.253694 5.017114 1.232141 +- 3.666601 5.213107 2.293908 +- 5.062354 5.920372 0.673198 +- 5.699537 6.377296 0.036552 +- 4.754312 6.389897 1.512695 ++ 5.005295 5.340406 0.315070 ++ 3.984875 5.817912 2.265912 ++ 4.408006 6.733705 2.314738 ++ 3.359598 5.504301 2.994456 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NASN.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -1130,13 +1130,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.220277 5.927344 0.433563 +- 4.913588 6.591689 1.420998 +- 6.050965 6.373808 -0.511346 +- 5.971268 7.107959 0.177690 +- 6.636748 6.497679 -1.324743 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.906966 5.848446 2.410297 ++ 3.138947 5.408353 3.262885 ++ 4.458847 7.061526 2.488328 ++ 4.248421 7.659050 3.274958 ++ 5.084275 7.376210 1.760376 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NGLN.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -1303,20 +1303,20 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.226485 5.898474 0.401698 +- 4.414018 6.624028 0.441300 +- 5.794506 5.938748 1.331123 +- 6.125319 6.253797 -0.719124 +- 6.688164 6.300372 -1.556463 +- 6.117846 7.301883 0.099632 +- 5.907135 8.163840 1.090353 +- 5.292210 7.913283 1.851398 +- 6.363014 9.065005 1.077109 +- 6.926823 7.627695 -0.904511 +- 7.501836 7.713669 -1.730386 +- 6.873063 8.384728 -0.238094 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.881095 5.817649 2.426715 ++ 2.801124 5.964886 2.435947 ++ 4.181612 5.279606 3.325770 ++ 4.540311 7.142726 2.424478 ++ 5.151800 7.375491 1.655062 ++ 4.364270 8.040994 3.389374 ++ 3.575005 7.807613 4.434120 ++ 3.088928 6.925430 4.508833 ++ 3.465343 8.513638 5.147984 ++ 5.006244 9.201290 3.286985 ++ 5.604850 9.375324 2.492326 ++ 4.892201 9.903050 4.004360 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NARG.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -1463,13 +1463,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.003504 6.072258 0.881472 +- 4.722990 6.580423 1.708019 +- 5.824163 6.508104 -0.056055 +- 5.654216 7.217462 0.753902 +- 6.562760 6.595751 -1.134430 +- 7.210678 6.375009 -2.309622 +- 7.387392 7.342143 -1.838959 ++ 3.942772 5.885090 2.382967 ++ 3.339711 5.691917 3.169798 ++ 4.624266 6.997644 2.182496 ++ 4.563036 7.811879 2.904557 ++ 5.294008 6.891449 1.061662 ++ 5.058971 5.678865 0.492455 ++ 5.537740 5.417840 -0.451339 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NHID.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -1609,13 +1609,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.003504 6.072258 0.881472 +- 5.824163 6.508104 -0.056055 +- 5.654216 7.217462 0.753902 +- 6.562760 6.595751 -1.134430 +- 6.629203 7.441424 -0.586231 +- 7.210678 6.375009 -2.309622 +- 7.387392 7.342143 -1.838959 ++ 3.942772 5.885090 2.382967 ++ 4.624266 6.997644 2.182496 ++ 4.563036 7.811879 2.904557 ++ 5.294008 6.891449 1.061662 ++ 5.896295 7.605082 0.676854 ++ 5.058971 5.678865 0.492455 ++ 5.537740 5.417840 -0.451339 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NHIE.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -1759,14 +1759,14 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.003504 6.072258 0.881472 +- 4.722990 6.580423 1.708019 +- 5.824163 6.508104 -0.056055 +- 5.654216 7.217462 0.753902 +- 6.562760 6.595751 -1.134430 +- 6.629203 7.441424 -0.586231 +- 7.210678 6.375009 -2.309622 +- 7.387392 7.342143 -1.838959 ++ 3.942772 5.885090 2.382967 ++ 3.339711 5.691917 3.169798 ++ 4.624266 6.997644 2.182496 ++ 4.563036 7.811879 2.904557 ++ 5.294008 6.891449 1.061662 ++ 5.896295 7.605082 0.676854 ++ 5.058971 5.678865 0.492455 ++ 5.537740 5.417840 -0.451339 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NHIP.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -1936,20 +1936,20 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 4.941957 6.093161 0.993054 +- 4.555798 6.518222 1.919501 +- 5.833674 6.587638 -0.009560 +- 5.727864 7.297382 0.701192 +- 6.577083 6.691104 -1.083216 +- 6.699953 7.881667 -0.356949 +- 7.350710 8.089828 -1.206234 +- 6.471604 8.773711 0.684306 +- 7.153163 9.167983 -0.069436 +- 6.163215 9.539474 1.752484 +- 6.850900 10.076243 1.098979 +- 5.726463 10.185215 2.927374 +- 6.404130 10.841773 2.381664 +- 5.125146 10.546906 4.138818 ++ 4.023443 5.931088 2.293236 ++ 3.368827 5.705470 3.135064 ++ 4.811936 7.073557 1.949805 ++ 4.882911 7.922013 2.493114 ++ 5.427345 6.842058 0.816764 ++ 6.297161 7.689048 0.119607 ++ 6.531228 8.676646 0.517052 ++ 6.814097 7.187003 -1.069017 ++ 7.498083 7.791848 -1.664355 ++ 6.482667 5.953109 -1.505090 ++ 6.897672 5.575635 -2.439640 ++ 5.604046 5.117349 -0.785625 ++ 5.358725 4.126563 -1.168065 ++ 5.083391 5.623006 0.411551 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NTRP.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -2108,16 +2108,16 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.021223 6.053049 0.839188 +- 4.662984 6.521610 1.755820 +- 5.904492 6.742286 -0.000329 +- 5.724114 7.440373 0.817130 +- 6.758713 7.099630 -1.050381 +- 6.738282 7.947511 -0.365705 +- 7.536653 7.157250 -2.212917 +- 7.655187 8.096815 -1.673224 +- 8.214242 6.953605 -3.420974 +- 8.451251 7.942064 -3.027432 ++ 3.911603 5.857254 2.409885 ++ 3.236109 5.513847 3.193390 ++ 4.490005 7.129516 2.492349 ++ 4.264839 7.776656 3.340058 ++ 5.357612 7.570590 1.486013 ++ 5.807939 8.561136 1.550217 ++ 5.646816 6.739401 0.397212 ++ 6.322310 7.082808 -0.386292 ++ 5.068414 5.467139 0.314748 ++ 5.293580 4.820000 -0.532961 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NPHE.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -2276,17 +2276,17 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.267323 4.996269 1.194944 +- 5.102503 5.984523 0.660315 +- 4.777863 6.502414 1.562811 +- 5.985574 6.611197 -0.227077 +- 5.846174 7.352316 0.559949 +- 6.824378 6.891857 -1.312267 +- 6.854321 7.991157 -0.512116 +- 6.305234 7.900783 0.270147 +- 7.573657 6.866032 -2.494602 +- 7.737299 7.827553 -2.007982 +- 8.211756 6.577405 -3.706841 +- 8.492629 7.576371 -3.373257 ++ 4.059917 5.918914 2.227275 ++ 3.400094 5.668222 3.057870 ++ 4.699989 7.163550 2.192787 ++ 4.538509 7.881896 2.996531 ++ 5.547468 7.485540 1.125968 ++ 6.169252 8.694615 1.092466 ++ 5.956320 9.246984 1.848209 ++ 5.754874 6.562895 0.093637 ++ 6.414696 6.813587 -0.736958 ++ 5.114801 5.318259 0.128125 ++ 5.276282 4.599913 -0.675619 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NTYR.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -2421,11 +2421,11 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.267323 4.996269 1.194944 +- 3.302423 5.493308 1.295046 +- 4.682911 4.808028 2.184869 +- 5.220383 5.890117 0.404729 +- 6.306867 5.987364 1.035359 +- 4.568248 6.850423 -0.085305 ++ 5.347407 4.849844 1.186161 ++ 3.966920 5.535124 0.296338 ++ 3.873721 5.805373 2.428701 ++ 4.594575 5.679017 3.454373 ++ 2.855955 6.542075 2.333709 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NGLU.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -2542,8 +2542,8 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.275095 5.011382 1.194525 +- 5.214909 5.080371 2.030940 +- 3.476290 5.943429 0.910275 ++ 3.669104 5.954940 0.620005 ++ 5.407723 5.091882 1.740669 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NASP.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -2697,18 +2697,18 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.226485 5.898474 0.401698 +- 4.414018 6.624028 0.441300 +- 5.794506 5.938748 1.331123 +- 6.145332 6.228186 -0.769897 +- 7.203874 5.974714 -0.827698 +- 5.823386 6.659994 -1.717522 +- 5.933539 7.203239 0.309601 +- 6.482814 7.265694 1.154880 +- 6.528435 7.362078 -0.491005 +- 5.203409 7.900796 0.330212 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.881095 5.817649 2.426715 ++ 2.801124 5.964886 2.435947 ++ 4.181612 5.279606 3.325770 ++ 4.578316 7.173413 2.389148 ++ 5.658401 7.026988 2.380365 ++ 4.277913 7.712268 1.490542 ++ 4.199407 7.952315 3.576852 ++ 4.478064 7.453372 4.409622 ++ 4.661173 8.850231 3.551971 ++ 3.198660 8.088474 3.584954 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NLYS.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -2838,11 +2838,11 @@ + 4.408167 0.002206 -0.902255 + 3.942020 -0.287863 0.790585 + 5.543318 1.147472 0.544698 +- 6.081407 2.093874 0.598404 +- 5.996931 0.515001 -0.218399 +- 5.523452 0.447794 1.882665 +- 6.357566 0.073964 1.288859 +- 5.873440 1.245104 2.538335 ++ 6.406713 0.710625 0.042886 ++ 5.648269 1.022234 1.622381 ++ 5.375452 2.604420 0.185221 ++ 5.701342 3.225018 1.019939 ++ 5.977270 2.833894 -0.694128 + 3.941702 2.857530 -0.104508 + 3.944087 3.337627 0.874062 + 2.888662 3.951879 -0.204456 +@@ -2964,9 +2964,9 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.309567 5.303525 1.366033 +- 5.145787 5.839753 0.481671 +- 4.563172 5.041444 1.938780 +- 3.657120 5.491212 1.354764 ++ 3.725381 5.622023 2.517634 ++ 4.051868 5.551722 0.788945 ++ 4.957920 5.101954 1.372960 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NCYS.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -3081,8 +3081,8 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.309567 5.303525 1.366033 +- 4.563172 5.041444 1.938780 +- 3.657120 5.491212 1.354764 ++ 4.051868 5.551722 0.788945 ++ 4.957920 5.101954 1.372960 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NCYX.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -3224,15 +3224,15 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.402881 6.076526 0.265157 +- 5.724538 5.972445 0.854008 +- 4.818486 6.422214 0.269993 +- 6.377314 6.105674 -1.224148 +- 6.034578 6.467191 -2.193651 +- 6.303017 6.908485 -0.490613 +- 7.415066 5.781911 -1.303828 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.817297 5.981271 2.651702 ++ 4.055297 5.545795 3.115122 ++ 3.149245 5.995564 2.531107 ++ 4.753204 7.463130 2.340945 ++ 4.433578 7.904044 1.396734 ++ 4.585895 8.175303 3.148978 ++ 5.814065 7.218764 2.286557 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NMET.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +diff -urN amber11.orig/AmberTools/test/sleap/oldleap/ff91/all_nucleic91.= lib.save amber11/AmberTools/test/sleap/oldleap/ff91/all_nucleic91.lib.sav= e +--- amber11.orig/AmberTools/test/sleap/oldleap/ff91/all_nucleic91.lib.sa= ve 2010-03-31 07:05:23.000000000 +0400 ++++ amber11/AmberTools/test/sleap/oldleap/ff91/all_nucleic91.lib.save 20= 11-03-08 16:38:44.000000000 +0300 +@@ -162,27 +162,27 @@ + 3.710733 0.830490 -3.744234 + 1.911850 1.246480 -4.585645 + 1.227112 2.479938 -4.747250 +- 1.435744 3.548600 -4.696894 +- 1.460583 2.154521 -6.213536 +- 0.611235 3.180043 -6.535735 +- -0.465186 3.098120 -6.567442 +- 1.349267 3.870896 -7.353068 +- -0.036082 3.758044 -7.339885 +- 0.351402 4.533174 -8.439444 +- -0.960336 4.612555 -8.701439 +- -1.624968 4.152050 -8.096212 +- -1.284404 5.132893 -9.504140 +- 1.216752 5.151275 -9.254748 +- -0.058580 5.292957 -9.604538 +- 0.617022 5.800159 -10.277374 +- -1.311694 5.457396 -9.985412 +- -2.648827 5.295295 -9.894316 ++ 1.476326 2.910069 -5.717291 ++ -0.266632 2.222549 -4.860734 ++ -1.220065 2.003738 -3.901574 ++ -0.944101 1.997212 -2.857447 ++ -2.424721 1.879538 -4.374202 ++ -2.264060 2.025899 -5.747107 ++ -3.171716 1.996442 -6.812608 ++ -4.488141 1.800018 -6.657550 ++ -4.872966 1.663197 -5.733813 ++ -5.095547 1.788787 -7.464416 ++ -2.681111 2.175962 -8.046577 ++ -1.373728 2.370469 -8.194275 ++ -0.957583 2.517234 -9.180015 ++ -0.428694 2.418225 -7.273933 ++ -0.949520 2.234705 -6.042040 + 2.953825 2.805883 -3.147902 + 2.001837 3.312549 -3.306355 + 1.598529 3.379160 -3.566738 + 1.132115 3.871151 -2.713214 + 1.786595 4.328794 -4.619224 +- 1.990348 5.218376 -4.321352 ++ 0.918045 4.664210 -4.853138 + 3.951586 3.479347 -3.901109 + !entry.RADE.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x + 1 30 0 0 0 0 +@@ -367,25 +367,25 @@ + 3.710733 0.830490 -3.744234 + 1.911850 1.246480 -4.585645 + 1.227112 2.479938 -4.747250 +- 1.435744 3.548600 -4.696894 +- 1.485202 2.137699 -6.174261 +- 0.655381 3.211408 -6.264512 +- -0.423435 3.161813 -6.254680 +- 1.273874 3.921103 -7.246041 +- 2.001469 4.404856 -7.897723 +- -0.138537 4.008754 -7.451742 +- 0.496986 4.687819 -8.388428 +- 1.506269 4.703628 -8.353806 +- -0.021913 5.169907 -9.108453 +- -1.467764 3.981289 -7.487821 +- -2.803489 3.801409 -7.305937 +- -2.649940 4.509819 -8.312007 ++ 1.476326 2.910069 -5.717291 ++ -0.230375 2.189658 -4.854806 ++ -0.988446 1.979043 -3.745496 ++ -0.535467 2.020843 -2.765974 ++ -2.318623 1.714239 -3.846032 ++ -2.910767 1.548015 -2.946124 ++ -2.871582 1.669472 -5.164035 ++ -4.156011 1.417550 -5.334852 ++ -4.717568 1.261374 -4.510012 ++ -4.549259 1.385324 -6.264593 ++ -2.122766 1.876681 -6.243498 ++ -0.794090 2.140091 -6.121697 ++ -0.063349 2.338641 -7.103631 + 2.953825 2.805883 -3.147902 + 3.277337 2.955353 -2.117806 + 1.598529 3.379160 -3.566738 + 1.132115 3.871151 -2.713214 + 1.786595 4.328794 -4.619224 +- 1.990348 5.218376 -4.321352 ++ 0.918045 4.664210 -4.853138 + 3.951586 3.479347 -3.901109 + !entry.RCYT.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x + 1 28 0 0 0 0 +@@ -581,28 +581,28 @@ + 3.710733 0.830490 -3.744234 + 1.911850 1.246480 -4.585645 + 1.227112 2.479938 -4.747250 +- 1.435744 3.548600 -4.696894 +- 1.485985 2.137078 -6.173971 +- 0.630205 3.182508 -6.455250 +- -0.447083 3.109089 -6.476705 +- 1.375610 3.824568 -7.320253 +- -0.009195 3.704817 -7.311681 +- 0.430021 4.484569 -8.414167 +- -0.743299 4.619666 -8.757634 +- 1.449094 5.077582 -9.169036 +- 2.230864 5.470422 -9.653301 +- 0.193424 5.321243 -9.687036 +- 1.134074 5.907027 -10.440452 +- 2.131730 5.897532 -10.283319 +- 0.809583 6.430577 -11.240890 +- -1.093830 5.428430 -10.003875 +- -2.446615 5.292973 -9.968886 ++ 1.476326 2.910069 -5.717291 ++ -0.230179 2.188641 -4.854706 ++ -1.148250 1.950412 -3.852312 ++ -0.834533 1.961464 -2.818939 ++ -2.363371 1.722968 -4.285727 ++ -2.247746 1.815662 -5.667805 ++ -3.226774 1.665775 -6.685370 ++ -4.425333 1.414365 -6.570704 ++ -2.671302 1.843175 -7.958154 ++ -3.284184 1.755160 -8.743412 ++ -1.346177 2.129674 -8.215759 ++ -1.013622 2.261923 -9.507083 ++ -1.624549 2.163147 -10.305276 ++ -0.043809 2.463028 -9.704869 ++ -0.430928 2.271846 -7.261291 ++ -0.954757 2.102421 -6.017708 + 2.953825 2.805883 -3.147902 + 3.277337 2.955353 -2.117806 + 1.598529 3.379160 -3.566738 + 1.132115 3.871151 -2.713214 + 1.786595 4.328794 -4.619224 +- 1.990348 5.218376 -4.321352 ++ 0.918045 4.664210 -4.853138 + 3.951586 3.479347 -3.901109 + !entry.RGUA.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x + 1 31 0 0 0 0 +@@ -876,24 +876,24 @@ + 3.710733 0.830490 -3.744234 + 1.911850 1.246480 -4.585645 + 1.227112 2.479938 -4.747250 +- 1.435744 3.548600 -4.696894 +- 1.462119 2.152380 -6.223183 +- 0.621409 3.225476 -6.359458 +- -0.457084 3.168437 -6.359671 +- 1.227187 3.969404 -7.294982 +- 1.951054 4.453936 -7.950226 +- -0.178556 4.113730 -7.571852 +- 0.321873 4.770160 -8.483756 +- -1.548942 3.990804 -7.465412 +- -1.150751 4.582332 -8.289814 +- -2.922393 3.884686 -7.383122 +- -2.754887 4.581962 -8.370112 ++ 1.476326 2.910069 -5.717291 ++ -0.276459 2.220856 -4.861481 ++ -1.084733 2.020834 -3.773554 ++ -0.665763 2.042111 -2.778360 ++ -2.406530 1.849990 -3.912354 ++ -3.030993 1.692292 -3.032992 ++ -3.019582 1.871650 -5.215158 ++ -4.219997 1.724488 -5.439315 ++ -2.132048 2.078389 -6.251470 ++ -2.549647 2.102845 -7.258005 ++ -0.768247 2.257235 -6.139841 ++ -0.062611 2.434266 -7.119196 + 2.953825 2.805883 -3.147902 + 3.102654 2.968023 -2.080353 + 1.598529 3.379160 -3.566738 + 1.132115 3.871151 -2.713214 + 1.786595 4.328794 -4.619224 +- 1.990348 5.218376 -4.321352 ++ 0.918045 4.664210 -4.853138 + 3.951586 3.479347 -3.901109 + !entry.RURA.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x + 1 27 0 0 0 0 +@@ -1080,21 +1080,21 @@ + 3.710733 0.830490 -3.744234 + 1.911850 1.246480 -4.585645 + 1.227112 2.479938 -4.747250 +- 1.435744 3.548600 -4.696894 +- 1.460583 2.154521 -6.213536 +- 0.611235 3.180043 -6.535735 +- -0.465186 3.098120 -6.567442 +- 1.349267 3.870896 -7.353068 +- -0.036082 3.758044 -7.339885 +- 0.351402 4.533174 -8.439444 +- -0.960336 4.612555 -8.701439 +- -1.624968 4.152050 -8.096212 +- -1.284404 5.132893 -9.504140 +- 1.216752 5.151275 -9.254748 +- -0.058580 5.292957 -9.604538 +- 0.617022 5.800159 -10.277374 +- -1.311694 5.457396 -9.985412 +- -2.648827 5.295295 -9.894316 ++ 1.476326 2.910069 -5.717291 ++ -0.266632 2.222549 -4.860734 ++ -1.220065 2.003738 -3.901574 ++ -0.944101 1.997212 -2.857447 ++ -2.424721 1.879538 -4.374202 ++ -2.264060 2.025899 -5.747107 ++ -3.171716 1.996442 -6.812608 ++ -4.488141 1.800018 -6.657550 ++ -4.872966 1.663197 -5.733813 ++ -5.095547 1.788787 -7.464416 ++ -2.681111 2.175962 -8.046577 ++ -1.373728 2.370469 -8.194275 ++ -0.957583 2.517234 -9.180015 ++ -0.428694 2.418225 -7.273933 ++ -0.949520 2.234705 -6.042040 + 2.953825 2.805883 -3.147902 + 3.102654 2.968023 -2.080353 + 1.598529 3.379160 -3.566738 +@@ -1279,19 +1279,19 @@ + 3.710733 0.830490 -3.744234 + 1.911850 1.246480 -4.585645 + 1.227112 2.479938 -4.747250 +- 1.435744 3.548600 -4.696894 +- 1.485202 2.137699 -6.174261 +- 0.655381 3.211408 -6.264512 +- -0.423435 3.161813 -6.254680 +- 1.273874 3.921103 -7.246041 +- 2.001469 4.404856 -7.897723 +- -0.138537 4.008754 -7.451742 +- 0.496986 4.687819 -8.388428 +- 1.506269 4.703628 -8.353806 +- -0.021913 5.169907 -9.108453 +- -1.467764 3.981289 -7.487821 +- -2.803489 3.801409 -7.305937 +- -2.649940 4.509819 -8.312007 ++ 1.476326 2.910069 -5.717291 ++ -0.230375 2.189658 -4.854806 ++ -0.988446 1.979043 -3.745496 ++ -0.535467 2.020843 -2.765974 ++ -2.318623 1.714239 -3.846032 ++ -2.910767 1.548015 -2.946124 ++ -2.871582 1.669472 -5.164035 ++ -4.156011 1.417550 -5.334852 ++ -4.717568 1.261374 -4.510012 ++ -4.549259 1.385324 -6.264593 ++ -2.122766 1.876681 -6.243498 ++ -0.794090 2.140091 -6.121697 ++ -0.063349 2.338641 -7.103631 + 2.953825 2.805883 -3.147902 + 3.277337 2.955353 -2.117806 + 1.598529 3.379160 -3.566738 +@@ -1487,22 +1487,22 @@ + 3.710733 0.830490 -3.744234 + 1.911850 1.246480 -4.585645 + 1.227112 2.479938 -4.747250 +- 1.435744 3.548600 -4.696894 +- 1.485985 2.137078 -6.173971 +- 0.630205 3.182508 -6.455250 +- -0.447083 3.109089 -6.476705 +- 1.375610 3.824568 -7.320253 +- -0.009195 3.704817 -7.311681 +- 0.430021 4.484569 -8.414167 +- -0.743299 4.619666 -8.757634 +- 1.449094 5.077582 -9.169036 +- 2.230864 5.470422 -9.653301 +- 0.193424 5.321243 -9.687036 +- 1.134074 5.907027 -10.440452 +- 2.131730 5.897532 -10.283319 +- 0.809583 6.430577 -11.240890 +- -1.093830 5.428430 -10.003875 +- -2.446615 5.292973 -9.968886 ++ 1.476326 2.910069 -5.717291 ++ -0.230179 2.188641 -4.854706 ++ -1.148250 1.950412 -3.852312 ++ -0.834533 1.961464 -2.818939 ++ -2.363371 1.722968 -4.285727 ++ -2.247746 1.815662 -5.667805 ++ -3.226774 1.665775 -6.685370 ++ -4.425333 1.414365 -6.570704 ++ -2.671302 1.843175 -7.958154 ++ -3.284184 1.755160 -8.743412 ++ -1.346177 2.129674 -8.215759 ++ -1.013622 2.261923 -9.507083 ++ -1.624549 2.163147 -10.305276 ++ -0.043809 2.463028 -9.704869 ++ -0.430928 2.271846 -7.261291 ++ -0.954757 2.102421 -6.017708 + 2.953825 2.805883 -3.147902 + 3.277337 2.955353 -2.117806 + 1.598529 3.379160 -3.566738 +@@ -1788,21 +1788,21 @@ + 3.710733 0.830490 -3.744234 + 1.911850 1.246480 -4.585645 + 1.227112 2.479938 -4.747250 +- 1.435744 3.548600 -4.696894 +- 1.462119 2.152380 -6.223183 +- 0.621409 3.225476 -6.359458 +- -0.457084 3.168437 -6.359671 +- 1.227187 3.969404 -7.294982 +- 2.191055 4.651430 -8.220076 +- 2.843927 3.908200 -8.677753 +- 1.638142 5.177191 -8.998511 +- 2.792502 5.365208 -7.657153 +- -0.178556 4.113730 -7.571852 +- 0.321873 4.770160 -8.483756 +- -1.548942 3.990804 -7.465412 +- -1.150751 4.582332 -8.289814 +- -2.922393 3.884686 -7.383122 +- -2.754887 4.581962 -8.370112 ++ 1.476326 2.910069 -5.717291 ++ -0.276459 2.220856 -4.861481 ++ -1.084733 2.020834 -3.773554 ++ -0.665763 2.042111 -2.778360 ++ -2.406530 1.849990 -3.912354 ++ -3.300021 1.630344 -2.727690 ++ -3.231144 2.486293 -2.056343 ++ -4.330132 1.515881 -3.065138 ++ -2.988981 0.729023 -2.199511 ++ -3.019582 1.871650 -5.215158 ++ -4.219997 1.724488 -5.439315 ++ -2.132048 2.078389 -6.251470 ++ -2.549647 2.102845 -7.258005 ++ -0.768247 2.257235 -6.139841 ++ -0.062611 2.434266 -7.119196 + 2.953825 2.805883 -3.147902 + 3.102654 2.968023 -2.080353 + 1.598529 3.379160 -3.566738 +diff -urN amber11.orig/AmberTools/test/sleap/oldleap/ff94/all_amino94.li= b.save amber11/AmberTools/test/sleap/oldleap/ff94/all_amino94.lib.save +--- amber11.orig/AmberTools/test/sleap/oldleap/ff94/all_amino94.lib.save= 2010-03-31 07:05:23.000000000 +0400 ++++ amber11/AmberTools/test/sleap/oldleap/ff94/all_amino94.lib.save 2011= -03-08 16:38:44.000000000 +0300 +@@ -260,7 +260,7 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.230747 4.925147 1.196914 +- 4.828085 5.500165 0.713033 ++ 3.983296 5.433818 1.972557 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.SER.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -372,7 +372,7 @@ + 1.784422 4.436955 2.124895 + 1.764698 4.397850 0.345787 + 3.971494 2.947416 2.411212 +- 4.374397 3.770738 2.696536 ++ 3.724043 3.456087 3.186855 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.THR.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -504,15 +504,15 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.857033 4.748192 2.579338 +- 5.821217 4.249596 2.480083 +- 4.990360 5.695010 3.102655 +- 4.176711 4.112860 3.146449 +- 5.226485 5.898474 0.401698 +- 5.794506 5.938748 1.331123 +- 5.883342 6.134649 -0.435476 +- 4.414018 6.624028 0.441300 ++ 5.354265 4.863179 1.185791 ++ 3.853427 5.762894 -0.062862 ++ 2.773446 5.910110 -0.054565 ++ 4.351509 6.732051 -0.090207 ++ 4.134162 5.185701 -0.943848 ++ 3.881095 5.817649 2.426715 ++ 4.181612 5.279606 3.325770 ++ 4.379188 6.786828 2.400358 ++ 2.801124 5.964886 2.435947 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.LEU.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -652,12 +652,12 @@ + 3.671552 3.399212 3.380613 + 3.485641 1.869279 2.490736 + 4.230199 4.986696 1.245167 +- 3.258221 5.469711 1.345449 +- 4.638709 4.784431 2.235272 +- 5.178160 5.906245 0.482655 +- 5.735477 5.933935 1.418994 +- 5.840562 6.170139 -0.341774 +- 4.354989 6.619215 0.529171 ++ 5.312304 4.855747 1.245167 ++ 3.931816 5.541027 0.355344 ++ 3.812283 5.761636 2.490333 ++ 4.110763 5.208108 3.380624 ++ 4.296680 6.738088 2.490828 ++ 2.730275 5.893388 2.490801 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.ILE.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -785,9 +785,9 @@ + 3.716963 3.477633 3.370556 + 3.499621 1.931327 2.516833 + 4.274181 5.009604 1.194574 +- 4.690774 4.823320 2.184447 +- 4.954792 5.645336 0.628258 +- 3.310286 5.508600 1.294624 ++ 3.973778 5.548459 0.295968 ++ 3.993550 5.587589 2.075074 ++ 5.354265 4.863179 1.185791 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.VAL.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -901,10 +901,10 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.253694 5.017114 1.232141 +- 3.666601 5.213107 2.293908 +- 5.062354 5.920372 0.673198 +- 5.699537 6.377296 0.036552 +- 4.754312 6.389897 1.512695 ++ 5.005295 5.340406 0.315070 ++ 3.984875 5.817912 2.265912 ++ 4.408006 6.733705 2.314738 ++ 3.359598 5.504301 2.994456 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.ASN.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -1028,13 +1028,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.220277 5.927344 0.433563 +- 4.913588 6.591689 1.420998 +- 6.050965 6.373808 -0.511346 +- 5.971268 7.107959 0.177690 +- 6.636748 6.497679 -1.324743 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.906966 5.848446 2.410297 ++ 3.138947 5.408353 3.262885 ++ 4.458847 7.061526 2.488328 ++ 4.248421 7.659050 3.274958 ++ 5.084275 7.376210 1.760376 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.GLN.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -1189,20 +1189,20 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.226485 5.898474 0.401698 +- 4.414018 6.624028 0.441300 +- 5.794506 5.938748 1.331123 +- 6.125319 6.253797 -0.719124 +- 6.688164 6.300372 -1.556463 +- 6.117846 7.301883 0.099632 +- 5.907135 8.163840 1.090353 +- 5.292210 7.913283 1.851398 +- 6.363014 9.065005 1.077109 +- 6.926823 7.627695 -0.904511 +- 7.501836 7.713669 -1.730386 +- 6.873063 8.384728 -0.238094 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.881095 5.817649 2.426715 ++ 2.801124 5.964886 2.435947 ++ 4.181612 5.279606 3.325770 ++ 4.540311 7.142726 2.424478 ++ 5.151800 7.375491 1.655062 ++ 4.364270 8.040994 3.389374 ++ 3.575005 7.807613 4.434120 ++ 3.088928 6.925430 4.508833 ++ 3.465343 8.513638 5.147984 ++ 5.006244 9.201290 3.286985 ++ 5.604850 9.375324 2.492326 ++ 4.892201 9.903050 4.004360 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.ARG.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -1337,13 +1337,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.003504 6.072258 0.881472 +- 4.722990 6.580423 1.708019 +- 5.824163 6.508104 -0.056055 +- 5.654216 7.217462 0.753902 +- 6.562760 6.595751 -1.134430 +- 7.210678 6.375009 -2.309622 +- 7.387392 7.342143 -1.838959 ++ 3.942772 5.885090 2.382967 ++ 3.339711 5.691917 3.169798 ++ 4.624266 6.997644 2.182496 ++ 4.563036 7.811879 2.904557 ++ 5.294008 6.891449 1.061662 ++ 5.058971 5.678865 0.492455 ++ 5.537740 5.417840 -0.451339 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.HID.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -1471,13 +1471,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.003504 6.072258 0.881472 +- 5.824163 6.508104 -0.056055 +- 5.654216 7.217462 0.753902 +- 6.562760 6.595751 -1.134430 +- 6.629203 7.441424 -0.586231 +- 7.210678 6.375009 -2.309622 +- 7.387392 7.342143 -1.838959 ++ 3.942772 5.885090 2.382967 ++ 4.624266 6.997644 2.182496 ++ 4.563036 7.811879 2.904557 ++ 5.294008 6.891449 1.061662 ++ 5.896295 7.605082 0.676854 ++ 5.058971 5.678865 0.492455 ++ 5.537740 5.417840 -0.451339 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.HIE.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -1609,14 +1609,14 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.003504 6.072258 0.881472 +- 4.722990 6.580423 1.708019 +- 5.824163 6.508104 -0.056055 +- 5.654216 7.217462 0.753902 +- 6.562760 6.595751 -1.134430 +- 6.629203 7.441424 -0.586231 +- 7.210678 6.375009 -2.309622 +- 7.387392 7.342143 -1.838959 ++ 3.942772 5.885090 2.382967 ++ 3.339711 5.691917 3.169798 ++ 4.624266 6.997644 2.182496 ++ 4.563036 7.811879 2.904557 ++ 5.294008 6.891449 1.061662 ++ 5.896295 7.605082 0.676854 ++ 5.058971 5.678865 0.492455 ++ 5.537740 5.417840 -0.451339 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.HIP.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -1774,20 +1774,20 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 4.941957 6.093161 0.993054 +- 4.555798 6.518222 1.919501 +- 5.833674 6.587638 -0.009560 +- 5.727864 7.297382 0.701192 +- 6.577083 6.691104 -1.083216 +- 6.699953 7.881667 -0.356949 +- 7.350710 8.089828 -1.206234 +- 6.471604 8.773711 0.684306 +- 7.153163 9.167983 -0.069436 +- 6.163215 9.539474 1.752484 +- 6.850900 10.076243 1.098979 +- 5.726463 10.185215 2.927374 +- 6.404130 10.841773 2.381664 +- 5.125146 10.546906 4.138818 ++ 4.023443 5.931088 2.293236 ++ 3.368827 5.705470 3.135064 ++ 4.811936 7.073557 1.949805 ++ 4.882911 7.922013 2.493114 ++ 5.427345 6.842058 0.816764 ++ 6.297161 7.689048 0.119607 ++ 6.531228 8.676646 0.517052 ++ 6.814097 7.187003 -1.069017 ++ 7.498083 7.791848 -1.664355 ++ 6.482667 5.953109 -1.505090 ++ 6.897672 5.575635 -2.439640 ++ 5.604046 5.117349 -0.785625 ++ 5.358725 4.126563 -1.168065 ++ 5.083391 5.623006 0.411551 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.TRP.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -1934,16 +1934,16 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.021223 6.053049 0.839188 +- 4.662984 6.521610 1.755820 +- 5.904492 6.742286 -0.000329 +- 5.724114 7.440373 0.817130 +- 6.758713 7.099630 -1.050381 +- 6.738282 7.947511 -0.365705 +- 7.536653 7.157250 -2.212917 +- 7.655187 8.096815 -1.673224 +- 8.214242 6.953605 -3.420974 +- 8.451251 7.942064 -3.027432 ++ 3.911603 5.857254 2.409885 ++ 3.236109 5.513847 3.193390 ++ 4.490005 7.129516 2.492349 ++ 4.264839 7.776656 3.340058 ++ 5.357612 7.570590 1.486013 ++ 5.807939 8.561136 1.550217 ++ 5.646816 6.739401 0.397212 ++ 6.322310 7.082808 -0.386292 ++ 5.068414 5.467139 0.314748 ++ 5.293580 4.820000 -0.532961 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.PHE.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -2090,17 +2090,17 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.267323 4.996269 1.194944 +- 5.102503 5.984523 0.660315 +- 4.777863 6.502414 1.562811 +- 5.985574 6.611197 -0.227077 +- 5.846174 7.352316 0.559949 +- 6.824378 6.891857 -1.312267 +- 6.854321 7.991157 -0.512116 +- 6.305234 7.900783 0.270147 +- 7.573657 6.866032 -2.494602 +- 7.737299 7.827553 -2.007982 +- 8.211756 6.577405 -3.706841 +- 8.492629 7.576371 -3.373257 ++ 4.059917 5.918914 2.227275 ++ 3.400094 5.668222 3.057870 ++ 4.699989 7.163550 2.192787 ++ 4.538509 7.881896 2.996531 ++ 5.547468 7.485540 1.125968 ++ 6.169252 8.694615 1.092466 ++ 5.956320 9.246984 1.848209 ++ 5.754874 6.562895 0.093637 ++ 6.414696 6.813587 -0.736958 ++ 5.114801 5.318259 0.128125 ++ 5.276282 4.599913 -0.675619 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.TYR.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -2223,11 +2223,11 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.267323 4.996269 1.194944 +- 3.302423 5.493308 1.295046 +- 4.682911 4.808028 2.184869 +- 5.220383 5.890117 0.404729 +- 6.306867 5.987364 1.035359 +- 4.568248 6.850423 -0.085305 ++ 5.347407 4.849844 1.186161 ++ 3.966920 5.535124 0.296338 ++ 3.873721 5.805373 2.428701 ++ 4.594575 5.679017 3.454373 ++ 2.855955 6.542075 2.333709 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.GLU.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -2332,8 +2332,8 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.275095 5.011382 1.194525 +- 5.214909 5.080371 2.030940 +- 3.476290 5.943429 0.910275 ++ 3.669104 5.954940 0.620005 ++ 5.407723 5.091882 1.740669 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.ASP.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -2475,18 +2475,18 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.226485 5.898474 0.401698 +- 4.414018 6.624028 0.441300 +- 5.794506 5.938748 1.331123 +- 6.145332 6.228186 -0.769897 +- 7.203874 5.974714 -0.827698 +- 5.823386 6.659994 -1.717522 +- 5.933539 7.203239 0.309601 +- 6.482814 7.265694 1.154880 +- 6.528435 7.362078 -0.491005 +- 5.203409 7.900796 0.330212 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.881095 5.817649 2.426715 ++ 2.801124 5.964886 2.435947 ++ 4.181612 5.279606 3.325770 ++ 4.578316 7.173413 2.389148 ++ 5.658401 7.026988 2.380365 ++ 4.277913 7.712268 1.490542 ++ 4.199407 7.952315 3.576852 ++ 4.478064 7.453372 4.409622 ++ 4.661173 8.850231 3.551971 ++ 3.198660 8.088474 3.584954 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.LYS.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -2634,17 +2634,17 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.226485 5.898474 0.401698 +- 4.414018 6.624028 0.441300 +- 5.794506 5.938748 1.331123 +- 6.145332 6.228186 -0.769897 +- 7.203874 5.974714 -0.827698 +- 5.823386 6.659994 -1.717522 +- 5.933539 7.203239 0.309601 +- 6.528435 7.362078 -0.491005 +- 5.203409 7.900796 0.330212 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.881095 5.817649 2.426715 ++ 2.801124 5.964886 2.435947 ++ 4.181612 5.279606 3.325770 ++ 4.578316 7.173413 2.389148 ++ 5.658401 7.026988 2.380365 ++ 4.277913 7.712268 1.490542 ++ 4.199407 7.952315 3.576852 ++ 4.661173 8.850231 3.551971 ++ 3.198660 8.088474 3.584954 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.LYN.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -2761,11 +2761,11 @@ + 4.419995 0.019280 -0.902255 + 3.955884 -0.274036 0.790585 + 5.547124 1.172442 0.544698 +- 6.078592 2.122578 0.598404 +- 6.005141 0.543154 -0.218399 +- 5.532142 0.472642 1.882665 +- 5.876555 1.272377 2.538335 +- 6.368845 0.104645 1.288859 ++ 6.413547 0.741633 0.042886 ++ 5.652946 1.047940 1.622381 ++ 5.369090 2.628183 0.185221 ++ 5.969291 2.861853 -0.694128 ++ 5.690639 3.251042 1.019939 + 3.933608 2.871277 -0.104508 + 3.611466 3.488572 0.734105 + 3.505165 3.526388 -1.409786 +@@ -2867,7 +2867,7 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.309567 5.303525 1.366033 +- 5.145787 5.839753 0.481671 ++ 3.725381 5.622023 2.517634 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.CYS.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -3079,13 +3079,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.402881 6.076526 0.265157 +- 6.377314 6.105674 -1.224148 +- 6.034578 6.467191 -2.193651 +- 6.303017 6.908485 -0.490613 +- 7.415066 5.781911 -1.303828 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.817297 5.981271 2.651702 ++ 4.753204 7.463130 2.340945 ++ 4.433578 7.904044 1.396734 ++ 4.585895 8.175303 3.148978 ++ 5.814065 7.218764 2.286557 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.MET.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -3196,9 +3196,9 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.275095 5.011382 1.194525 +- 5.214909 5.080371 2.030940 +- 3.476290 5.943429 0.910275 +- 4.245574 6.470767 0.682862 ++ 3.669104 5.954940 0.620005 ++ 5.407723 5.091882 1.740669 ++ 5.742895 5.987180 1.652921 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.ASH.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -3317,12 +3317,12 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.267323 4.996269 1.194944 +- 3.302423 5.493308 1.295046 +- 4.682911 4.808028 2.184869 +- 5.220383 5.890117 0.404729 +- 6.306867 5.987364 1.035359 +- 4.568248 6.850423 -0.085305 +- 5.508873 7.035106 -0.033194 ++ 5.347407 4.849844 1.186161 ++ 3.966920 5.535124 0.296338 ++ 3.873721 5.805373 2.428701 ++ 4.594575 5.679017 3.454373 ++ 2.855955 6.542075 2.333709 ++ 2.710512 6.996629 3.166671 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.GLH.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +diff -urN amber11.orig/AmberTools/test/sleap/oldleap/ff94/all_aminoct94.= lib.save amber11/AmberTools/test/sleap/oldleap/ff94/all_aminoct94.lib.sav= e +--- amber11.orig/AmberTools/test/sleap/oldleap/ff94/all_aminoct94.lib.sa= ve 2010-03-31 07:05:23.000000000 +0400 ++++ amber11/AmberTools/test/sleap/oldleap/ff94/all_aminoct94.lib.save 20= 11-03-08 16:38:44.000000000 +0300 +@@ -272,7 +272,7 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.230747 4.925147 1.196914 +- 4.828085 5.500165 0.713033 ++ 3.983296 5.433818 1.972557 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -390,7 +390,7 @@ + 1.784422 4.436955 2.124895 + 1.764698 4.397850 0.345787 + 3.971494 2.947416 2.411212 +- 4.374397 3.770738 2.696536 ++ 3.724043 3.456087 3.186855 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -528,15 +528,15 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.857033 4.748192 2.579338 +- 5.821217 4.249596 2.480083 +- 4.990360 5.695010 3.102655 +- 4.176711 4.112860 3.146449 +- 5.226485 5.898474 0.401698 +- 5.794506 5.938748 1.331123 +- 5.883342 6.134649 -0.435476 +- 4.414018 6.624028 0.441300 ++ 5.354265 4.863179 1.185791 ++ 3.853427 5.762894 -0.062862 ++ 2.773446 5.910110 -0.054565 ++ 4.351509 6.732051 -0.090207 ++ 4.134162 5.185701 -0.943848 ++ 3.881095 5.817649 2.426715 ++ 4.181612 5.279606 3.325770 ++ 4.379188 6.786828 2.400358 ++ 2.801124 5.964886 2.435947 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -682,12 +682,12 @@ + 3.671552 3.399212 3.380613 + 3.485641 1.869279 2.490736 + 4.230199 4.986696 1.245167 +- 3.258221 5.469711 1.345449 +- 4.638709 4.784431 2.235272 +- 5.178160 5.906245 0.482655 +- 5.735477 5.933935 1.418994 +- 5.840562 6.170139 -0.341774 +- 4.354989 6.619215 0.529171 ++ 5.312304 4.855747 1.245167 ++ 3.931816 5.541027 0.355344 ++ 3.812283 5.761636 2.490333 ++ 4.110763 5.208108 3.380624 ++ 4.296680 6.738088 2.490828 ++ 2.730275 5.893388 2.490801 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -821,9 +821,9 @@ + 3.716963 3.477633 3.370556 + 3.499621 1.931327 2.516833 + 4.274181 5.009604 1.194574 +- 4.690774 4.823320 2.184447 +- 4.954792 5.645336 0.628258 +- 3.310286 5.508600 1.294624 ++ 3.973778 5.548459 0.295968 ++ 3.993550 5.587589 2.075074 ++ 5.354265 4.863179 1.185791 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -943,10 +943,10 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.253694 5.017114 1.232141 +- 3.666601 5.213107 2.293908 +- 5.062354 5.920372 0.673198 +- 5.699537 6.377296 0.036552 +- 4.754312 6.389897 1.512695 ++ 5.005295 5.340406 0.315070 ++ 3.984875 5.817912 2.265912 ++ 4.408006 6.733705 2.314738 ++ 3.359598 5.504301 2.994456 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -1076,13 +1076,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.220277 5.927344 0.433563 +- 4.913588 6.591689 1.420998 +- 6.050965 6.373808 -0.511346 +- 5.971268 7.107959 0.177690 +- 6.636748 6.497679 -1.324743 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.906966 5.848446 2.410297 ++ 3.138947 5.408353 3.262885 ++ 4.458847 7.061526 2.488328 ++ 4.248421 7.659050 3.274958 ++ 5.084275 7.376210 1.760376 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -1243,20 +1243,20 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.226485 5.898474 0.401698 +- 4.414018 6.624028 0.441300 +- 5.794506 5.938748 1.331123 +- 6.125319 6.253797 -0.719124 +- 6.688164 6.300372 -1.556463 +- 6.117846 7.301883 0.099632 +- 5.907135 8.163840 1.090353 +- 5.292210 7.913283 1.851398 +- 6.363014 9.065005 1.077109 +- 6.926823 7.627695 -0.904511 +- 7.501836 7.713669 -1.730386 +- 6.873063 8.384728 -0.238094 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.881095 5.817649 2.426715 ++ 2.801124 5.964886 2.435947 ++ 4.181612 5.279606 3.325770 ++ 4.540311 7.142726 2.424478 ++ 5.151800 7.375491 1.655062 ++ 4.364270 8.040994 3.389374 ++ 3.575005 7.807613 4.434120 ++ 3.088928 6.925430 4.508833 ++ 3.465343 8.513638 5.147984 ++ 5.006244 9.201290 3.286985 ++ 5.604850 9.375324 2.492326 ++ 4.892201 9.903050 4.004360 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -1397,13 +1397,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.003504 6.072258 0.881472 +- 4.722990 6.580423 1.708019 +- 5.824163 6.508104 -0.056055 +- 5.654216 7.217462 0.753902 +- 6.562760 6.595751 -1.134430 +- 7.210678 6.375009 -2.309622 +- 7.387392 7.342143 -1.838959 ++ 3.942772 5.885090 2.382967 ++ 3.339711 5.691917 3.169798 ++ 4.624266 6.997644 2.182496 ++ 4.563036 7.811879 2.904557 ++ 5.294008 6.891449 1.061662 ++ 5.058971 5.678865 0.492455 ++ 5.537740 5.417840 -0.451339 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -1537,13 +1537,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.003504 6.072258 0.881472 +- 5.824163 6.508104 -0.056055 +- 5.654216 7.217462 0.753902 +- 6.562760 6.595751 -1.134430 +- 6.629203 7.441424 -0.586231 +- 7.210678 6.375009 -2.309622 +- 7.387392 7.342143 -1.838959 ++ 3.942772 5.885090 2.382967 ++ 4.624266 6.997644 2.182496 ++ 4.563036 7.811879 2.904557 ++ 5.294008 6.891449 1.061662 ++ 5.896295 7.605082 0.676854 ++ 5.058971 5.678865 0.492455 ++ 5.537740 5.417840 -0.451339 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -1681,14 +1681,14 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.003504 6.072258 0.881472 +- 4.722990 6.580423 1.708019 +- 5.824163 6.508104 -0.056055 +- 5.654216 7.217462 0.753902 +- 6.562760 6.595751 -1.134430 +- 6.629203 7.441424 -0.586231 +- 7.210678 6.375009 -2.309622 +- 7.387392 7.342143 -1.838959 ++ 3.942772 5.885090 2.382967 ++ 3.339711 5.691917 3.169798 ++ 4.624266 6.997644 2.182496 ++ 4.563036 7.811879 2.904557 ++ 5.294008 6.891449 1.061662 ++ 5.896295 7.605082 0.676854 ++ 5.058971 5.678865 0.492455 ++ 5.537740 5.417840 -0.451339 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -1852,20 +1852,20 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 4.941957 6.093161 0.993054 +- 4.555798 6.518222 1.919501 +- 5.833674 6.587638 -0.009560 +- 5.727864 7.297382 0.701192 +- 6.577083 6.691104 -1.083216 +- 6.699953 7.881667 -0.356949 +- 7.350710 8.089828 -1.206234 +- 6.471604 8.773711 0.684306 +- 7.153163 9.167983 -0.069436 +- 6.163215 9.539474 1.752484 +- 6.850900 10.076243 1.098979 +- 5.726463 10.185215 2.927374 +- 6.404130 10.841773 2.381664 +- 5.125146 10.546906 4.138818 ++ 4.023443 5.931088 2.293236 ++ 3.368827 5.705470 3.135064 ++ 4.811936 7.073557 1.949805 ++ 4.882911 7.922013 2.493114 ++ 5.427345 6.842058 0.816764 ++ 6.297161 7.689048 0.119607 ++ 6.531228 8.676646 0.517052 ++ 6.814097 7.187003 -1.069017 ++ 7.498083 7.791848 -1.664355 ++ 6.482667 5.953109 -1.505090 ++ 6.897672 5.575635 -2.439640 ++ 5.604046 5.117349 -0.785625 ++ 5.358725 4.126563 -1.168065 ++ 5.083391 5.623006 0.411551 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -2018,16 +2018,16 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.021223 6.053049 0.839188 +- 4.662984 6.521610 1.755820 +- 5.904492 6.742286 -0.000329 +- 5.724114 7.440373 0.817130 +- 6.758713 7.099630 -1.050381 +- 6.738282 7.947511 -0.365705 +- 7.536653 7.157250 -2.212917 +- 7.655187 8.096815 -1.673224 +- 8.214242 6.953605 -3.420974 +- 8.451251 7.942064 -3.027432 ++ 3.911603 5.857254 2.409885 ++ 3.236109 5.513847 3.193390 ++ 4.490005 7.129516 2.492349 ++ 4.264839 7.776656 3.340058 ++ 5.357612 7.570590 1.486013 ++ 5.807939 8.561136 1.550217 ++ 5.646816 6.739401 0.397212 ++ 6.322310 7.082808 -0.386292 ++ 5.068414 5.467139 0.314748 ++ 5.293580 4.820000 -0.532961 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -2180,17 +2180,17 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.267323 4.996269 1.194944 +- 5.102503 5.984523 0.660315 +- 4.777863 6.502414 1.562811 +- 5.985574 6.611197 -0.227077 +- 5.846174 7.352316 0.559949 +- 6.824378 6.891857 -1.312267 +- 6.854321 7.991157 -0.512116 +- 6.305234 7.900783 0.270147 +- 7.573657 6.866032 -2.494602 +- 7.737299 7.827553 -2.007982 +- 8.211756 6.577405 -3.706841 +- 8.492629 7.576371 -3.373257 ++ 4.059917 5.918914 2.227275 ++ 3.400094 5.668222 3.057870 ++ 4.699989 7.163550 2.192787 ++ 4.538509 7.881896 2.996531 ++ 5.547468 7.485540 1.125968 ++ 6.169252 8.694615 1.092466 ++ 5.956320 9.246984 1.848209 ++ 5.754874 6.562895 0.093637 ++ 6.414696 6.813587 -0.736958 ++ 5.114801 5.318259 0.128125 ++ 5.276282 4.599913 -0.675619 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -2319,11 +2319,11 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.267323 4.996269 1.194944 +- 3.302423 5.493308 1.295046 +- 4.682911 4.808028 2.184869 +- 5.220383 5.890117 0.404729 +- 6.306867 5.987364 1.035359 +- 4.568248 6.850423 -0.085305 ++ 5.347407 4.849844 1.186161 ++ 3.966920 5.535124 0.296338 ++ 3.873721 5.805373 2.428701 ++ 4.594575 5.679017 3.454373 ++ 2.855955 6.542075 2.333709 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -2434,8 +2434,8 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.275095 5.011382 1.194525 +- 5.214909 5.080371 2.030940 +- 3.476290 5.943429 0.910275 ++ 3.669104 5.954940 0.620005 ++ 5.407723 5.091882 1.740669 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -2583,18 +2583,18 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.226485 5.898474 0.401698 +- 4.414018 6.624028 0.441300 +- 5.794506 5.938748 1.331123 +- 6.145332 6.228186 -0.769897 +- 7.203874 5.974714 -0.827698 +- 5.823386 6.659994 -1.717522 +- 5.933539 7.203239 0.309601 +- 6.482814 7.265694 1.154880 +- 6.528435 7.362078 -0.491005 +- 5.203409 7.900796 0.330212 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.881095 5.817649 2.426715 ++ 2.801124 5.964886 2.435947 ++ 4.181612 5.279606 3.325770 ++ 4.578316 7.173413 2.389148 ++ 5.658401 7.026988 2.380365 ++ 4.277913 7.712268 1.490542 ++ 4.199407 7.952315 3.576852 ++ 4.478064 7.453372 4.409622 ++ 4.661173 8.850231 3.551971 ++ 3.198660 8.088474 3.584954 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -2718,11 +2718,11 @@ + 4.419995 0.019280 -0.902255 + 3.955884 -0.274036 0.790585 + 5.547124 1.172442 0.544698 +- 6.078592 2.122578 0.598404 +- 6.005141 0.543154 -0.218399 +- 5.532142 0.472642 1.882665 +- 5.876555 1.272377 2.538335 +- 6.368845 0.104645 1.288859 ++ 6.413547 0.741633 0.042886 ++ 5.652946 1.047940 1.622381 ++ 5.369090 2.628183 0.185221 ++ 5.969291 2.861853 -0.694128 ++ 5.690639 3.251042 1.019939 + 3.933608 2.871277 -0.104508 + 3.611466 3.488572 0.734105 + 3.505165 3.526388 -1.409786 +@@ -2830,7 +2830,7 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.309567 5.303525 1.366033 +- 5.145787 5.839753 0.481671 ++ 3.725381 5.622023 2.517634 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +@@ -3054,13 +3054,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.402881 6.076526 0.265157 +- 6.377314 6.105674 -1.224148 +- 6.034578 6.467191 -2.193651 +- 6.303017 6.908485 -0.490613 +- 7.415066 5.781911 -1.303828 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.817297 5.981271 2.651702 ++ 4.753204 7.463130 2.340945 ++ 4.433578 7.904044 1.396734 ++ 4.585895 8.175303 3.148978 ++ 5.814065 7.218764 2.286557 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + 6.204451 3.702005 0.000000 +diff -urN amber11.orig/AmberTools/test/sleap/oldleap/ff94/all_aminont94.= lib.save amber11/AmberTools/test/sleap/oldleap/ff94/all_aminont94.lib.sav= e +--- amber11.orig/AmberTools/test/sleap/oldleap/ff94/all_aminont94.lib.sa= ve 2010-03-31 07:05:23.000000000 +0400 ++++ amber11/AmberTools/test/sleap/oldleap/ff94/all_aminont94.lib.save 20= 11-03-08 16:38:44.000000000 +0300 +@@ -290,7 +290,7 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.230747 4.925147 1.196914 +- 4.828085 5.500165 0.713033 ++ 3.983296 5.433818 1.972557 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NSER.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -414,7 +414,7 @@ + 1.784422 4.436955 2.124895 + 1.764698 4.397850 0.345787 + 3.971494 2.947416 2.411212 +- 4.374397 3.770738 2.696536 ++ 3.724043 3.456087 3.186855 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NTHR.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -558,15 +558,15 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.857033 4.748192 2.579338 +- 5.821217 4.249596 2.480083 +- 4.990360 5.695010 3.102655 +- 4.176711 4.112860 3.146449 +- 5.226485 5.898474 0.401698 +- 5.794506 5.938748 1.331123 +- 5.883342 6.134649 -0.435476 +- 4.414018 6.624028 0.441300 ++ 5.354265 4.863179 1.185791 ++ 3.853427 5.762894 -0.062862 ++ 2.773446 5.910110 -0.054565 ++ 4.351509 6.732051 -0.090207 ++ 4.134162 5.185701 -0.943848 ++ 3.881095 5.817649 2.426715 ++ 4.181612 5.279606 3.325770 ++ 4.379188 6.786828 2.400358 ++ 2.801124 5.964886 2.435947 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NLEU.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -718,12 +718,12 @@ + 3.671552 3.399212 3.380613 + 3.485641 1.869279 2.490736 + 4.230199 4.986696 1.245167 +- 4.638709 4.784431 2.235272 +- 3.258221 5.469711 1.345449 +- 5.178160 5.906245 0.482655 +- 5.735477 5.933935 1.418994 +- 5.840562 6.170139 -0.341774 +- 4.354989 6.619215 0.529171 ++ 3.931816 5.541027 0.355344 ++ 5.312304 4.855747 1.245167 ++ 3.812283 5.761636 2.490333 ++ 4.110763 5.208108 3.380624 ++ 4.296680 6.738088 2.490828 ++ 2.730275 5.893388 2.490801 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NILE.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -863,9 +863,9 @@ + 3.716963 3.477633 3.370556 + 3.499621 1.931327 2.516833 + 4.274181 5.009604 1.194574 +- 4.690774 4.823320 2.184447 +- 4.954792 5.645336 0.628258 +- 3.310286 5.508600 1.294624 ++ 3.973778 5.548459 0.295968 ++ 3.993550 5.587589 2.075074 ++ 5.354265 4.863179 1.185791 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NVAL.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -991,10 +991,10 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.253694 5.017114 1.232141 +- 3.666601 5.213107 2.293908 +- 5.062354 5.920372 0.673198 +- 5.699537 6.377296 0.036552 +- 4.754312 6.389897 1.512695 ++ 5.005295 5.340406 0.315070 ++ 3.984875 5.817912 2.265912 ++ 4.408006 6.733705 2.314738 ++ 3.359598 5.504301 2.994456 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NASN.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -1130,13 +1130,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.220277 5.927344 0.433563 +- 4.913588 6.591689 1.420998 +- 6.050965 6.373808 -0.511346 +- 5.971268 7.107959 0.177690 +- 6.636748 6.497679 -1.324743 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.906966 5.848446 2.410297 ++ 3.138947 5.408353 3.262885 ++ 4.458847 7.061526 2.488328 ++ 4.248421 7.659050 3.274958 ++ 5.084275 7.376210 1.760376 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NGLN.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -1303,20 +1303,20 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.226485 5.898474 0.401698 +- 4.414018 6.624028 0.441300 +- 5.794506 5.938748 1.331123 +- 6.125319 6.253797 -0.719124 +- 6.688164 6.300372 -1.556463 +- 6.117846 7.301883 0.099632 +- 5.907135 8.163840 1.090353 +- 5.292210 7.913283 1.851398 +- 6.363014 9.065005 1.077109 +- 6.926823 7.627695 -0.904511 +- 7.501836 7.713669 -1.730386 +- 6.873063 8.384728 -0.238094 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.881095 5.817649 2.426715 ++ 2.801124 5.964886 2.435947 ++ 4.181612 5.279606 3.325770 ++ 4.540311 7.142726 2.424478 ++ 5.151800 7.375491 1.655062 ++ 4.364270 8.040994 3.389374 ++ 3.575005 7.807613 4.434120 ++ 3.088928 6.925430 4.508833 ++ 3.465343 8.513638 5.147984 ++ 5.006244 9.201290 3.286985 ++ 5.604850 9.375324 2.492326 ++ 4.892201 9.903050 4.004360 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NARG.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -1463,13 +1463,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.003504 6.072258 0.881472 +- 4.722990 6.580423 1.708019 +- 5.824163 6.508104 -0.056055 +- 5.654216 7.217462 0.753902 +- 6.562760 6.595751 -1.134430 +- 7.210678 6.375009 -2.309622 +- 7.387392 7.342143 -1.838959 ++ 3.942772 5.885090 2.382967 ++ 3.339711 5.691917 3.169798 ++ 4.624266 6.997644 2.182496 ++ 4.563036 7.811879 2.904557 ++ 5.294008 6.891449 1.061662 ++ 5.058971 5.678865 0.492455 ++ 5.537740 5.417840 -0.451339 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NHID.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -1609,13 +1609,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.003504 6.072258 0.881472 +- 5.824163 6.508104 -0.056055 +- 5.654216 7.217462 0.753902 +- 6.562760 6.595751 -1.134430 +- 6.629203 7.441424 -0.586231 +- 7.210678 6.375009 -2.309622 +- 7.387392 7.342143 -1.838959 ++ 3.942772 5.885090 2.382967 ++ 4.624266 6.997644 2.182496 ++ 4.563036 7.811879 2.904557 ++ 5.294008 6.891449 1.061662 ++ 5.896295 7.605082 0.676854 ++ 5.058971 5.678865 0.492455 ++ 5.537740 5.417840 -0.451339 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NHIE.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -1759,14 +1759,14 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.003504 6.072258 0.881472 +- 4.722990 6.580423 1.708019 +- 5.824163 6.508104 -0.056055 +- 5.654216 7.217462 0.753902 +- 6.562760 6.595751 -1.134430 +- 6.629203 7.441424 -0.586231 +- 7.210678 6.375009 -2.309622 +- 7.387392 7.342143 -1.838959 ++ 3.942772 5.885090 2.382967 ++ 3.339711 5.691917 3.169798 ++ 4.624266 6.997644 2.182496 ++ 4.563036 7.811879 2.904557 ++ 5.294008 6.891449 1.061662 ++ 5.896295 7.605082 0.676854 ++ 5.058971 5.678865 0.492455 ++ 5.537740 5.417840 -0.451339 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NHIP.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -1936,20 +1936,20 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 4.941957 6.093161 0.993054 +- 4.555798 6.518222 1.919501 +- 5.833674 6.587638 -0.009560 +- 5.727864 7.297382 0.701192 +- 6.577083 6.691104 -1.083216 +- 6.699953 7.881667 -0.356949 +- 7.350710 8.089828 -1.206234 +- 6.471604 8.773711 0.684306 +- 7.153163 9.167983 -0.069436 +- 6.163215 9.539474 1.752484 +- 6.850900 10.076243 1.098979 +- 5.726463 10.185215 2.927374 +- 6.404130 10.841773 2.381664 +- 5.125146 10.546906 4.138818 ++ 4.023443 5.931088 2.293236 ++ 3.368827 5.705470 3.135064 ++ 4.811936 7.073557 1.949805 ++ 4.882911 7.922013 2.493114 ++ 5.427345 6.842058 0.816764 ++ 6.297161 7.689048 0.119607 ++ 6.531228 8.676646 0.517052 ++ 6.814097 7.187003 -1.069017 ++ 7.498083 7.791848 -1.664355 ++ 6.482667 5.953109 -1.505090 ++ 6.897672 5.575635 -2.439640 ++ 5.604046 5.117349 -0.785625 ++ 5.358725 4.126563 -1.168065 ++ 5.083391 5.623006 0.411551 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NTRP.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -2108,16 +2108,16 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.200807 5.026066 1.321085 +- 5.021223 6.053049 0.839188 +- 4.662984 6.521610 1.755820 +- 5.904492 6.742286 -0.000329 +- 5.724114 7.440373 0.817130 +- 6.758713 7.099630 -1.050381 +- 6.738282 7.947511 -0.365705 +- 7.536653 7.157250 -2.212917 +- 7.655187 8.096815 -1.673224 +- 8.214242 6.953605 -3.420974 +- 8.451251 7.942064 -3.027432 ++ 3.911603 5.857254 2.409885 ++ 3.236109 5.513847 3.193390 ++ 4.490005 7.129516 2.492349 ++ 4.264839 7.776656 3.340058 ++ 5.357612 7.570590 1.486013 ++ 5.807939 8.561136 1.550217 ++ 5.646816 6.739401 0.397212 ++ 6.322310 7.082808 -0.386292 ++ 5.068414 5.467139 0.314748 ++ 5.293580 4.820000 -0.532961 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NPHE.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -2276,17 +2276,17 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.267323 4.996269 1.194944 +- 5.102503 5.984523 0.660315 +- 4.777863 6.502414 1.562811 +- 5.985574 6.611197 -0.227077 +- 5.846174 7.352316 0.559949 +- 6.824378 6.891857 -1.312267 +- 6.854321 7.991157 -0.512116 +- 6.305234 7.900783 0.270147 +- 7.573657 6.866032 -2.494602 +- 7.737299 7.827553 -2.007982 +- 8.211756 6.577405 -3.706841 +- 8.492629 7.576371 -3.373257 ++ 4.059917 5.918914 2.227275 ++ 3.400094 5.668222 3.057870 ++ 4.699989 7.163550 2.192787 ++ 4.538509 7.881896 2.996531 ++ 5.547468 7.485540 1.125968 ++ 6.169252 8.694615 1.092466 ++ 5.956320 9.246984 1.848209 ++ 5.754874 6.562895 0.093637 ++ 6.414696 6.813587 -0.736958 ++ 5.114801 5.318259 0.128125 ++ 5.276282 4.599913 -0.675619 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NTYR.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -2421,11 +2421,11 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.267323 4.996269 1.194944 +- 3.302423 5.493308 1.295046 +- 4.682911 4.808028 2.184869 +- 5.220383 5.890117 0.404729 +- 6.306867 5.987364 1.035359 +- 4.568248 6.850423 -0.085305 ++ 5.347407 4.849844 1.186161 ++ 3.966920 5.535124 0.296338 ++ 3.873721 5.805373 2.428701 ++ 4.594575 5.679017 3.454373 ++ 2.855955 6.542075 2.333709 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NGLU.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -2542,8 +2542,8 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.275095 5.011382 1.194525 +- 5.214909 5.080371 2.030940 +- 3.476290 5.943429 0.910275 ++ 3.669104 5.954940 0.620005 ++ 5.407723 5.091882 1.740669 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NASP.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -2697,18 +2697,18 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.226485 5.898474 0.401698 +- 4.414018 6.624028 0.441300 +- 5.794506 5.938748 1.331123 +- 6.145332 6.228186 -0.769897 +- 7.203874 5.974714 -0.827698 +- 5.823386 6.659994 -1.717522 +- 5.933539 7.203239 0.309601 +- 6.482814 7.265694 1.154880 +- 6.528435 7.362078 -0.491005 +- 5.203409 7.900796 0.330212 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.881095 5.817649 2.426715 ++ 2.801124 5.964886 2.435947 ++ 4.181612 5.279606 3.325770 ++ 4.578316 7.173413 2.389148 ++ 5.658401 7.026988 2.380365 ++ 4.277913 7.712268 1.490542 ++ 4.199407 7.952315 3.576852 ++ 4.478064 7.453372 4.409622 ++ 4.661173 8.850231 3.551971 ++ 3.198660 8.088474 3.584954 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NLYS.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -2838,11 +2838,11 @@ + 4.408167 0.002206 -0.902255 + 3.942020 -0.287863 0.790585 + 5.543318 1.147472 0.544698 +- 6.081407 2.093874 0.598404 +- 5.996931 0.515001 -0.218399 +- 5.523452 0.447794 1.882665 +- 5.873440 1.245104 2.538335 +- 6.357566 0.073964 1.288859 ++ 6.406713 0.710625 0.042886 ++ 5.648269 1.022234 1.622381 ++ 5.375452 2.604420 0.185221 ++ 5.977270 2.833894 -0.694128 ++ 5.701342 3.225018 1.019939 + 3.941702 2.857530 -0.104508 + 3.623877 3.477058 0.734105 + 3.517843 3.515616 -1.409786 +@@ -2956,7 +2956,7 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.309567 5.303525 1.366033 +- 5.145787 5.839753 0.481671 ++ 3.725381 5.622023 2.517634 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NCYS.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +@@ -3192,13 +3192,13 @@ + 2.496989 3.801078 1.241373 + 3.877477 3.115798 2.131196 + 4.274181 5.009604 1.194574 +- 3.310286 5.508600 1.294624 +- 4.690774 4.823320 2.184447 +- 5.402881 6.076526 0.265157 +- 6.377314 6.105674 -1.224148 +- 6.034578 6.467191 -2.193651 +- 6.303017 6.908485 -0.490613 +- 7.415066 5.781911 -1.303828 ++ 5.354265 4.863179 1.185791 ++ 3.973778 5.548459 0.295968 ++ 3.817297 5.981271 2.651702 ++ 4.753204 7.463130 2.340945 ++ 4.433578 7.904044 1.396734 ++ 4.585895 8.175303 3.148978 ++ 5.814065 7.218764 2.286557 + 5.485538 2.705208 0.000000 + 6.008821 1.593175 0.000000 + !entry.NMET.unit.residueconnect table int c1x int c2x int c3x int c= 4x int c5x int c6x +diff -urN amber11.orig/AmberTools/test/sleap/oldleap/ff94/all_nucleic94.= lib.save amber11/AmberTools/test/sleap/oldleap/ff94/all_nucleic94.lib.sav= e +--- amber11.orig/AmberTools/test/sleap/oldleap/ff94/all_nucleic94.lib.sa= ve 2010-03-31 07:05:23.000000000 +0400 ++++ amber11/AmberTools/test/sleap/oldleap/ff94/all_nucleic94.lib.save 20= 11-03-08 16:38:44.000000000 +0300 +@@ -181,21 +181,21 @@ + 0.391890 3.029890 3.571783 + 1.142222 1.169994 3.879663 + 2.468198 0.737932 4.147078 +- 3.422991 1.160472 4.460013 +- 1.825854 0.331961 5.463505 +- 2.973744 -0.351218 5.767666 +- 3.198298 -1.353172 5.432908 +- 3.262456 0.147686 6.932887 +- 3.554407 -1.123002 6.450998 +- 3.970615 -1.030384 7.784487 +- 4.371751 -2.299375 7.628436 +- 4.806122 -2.789852 8.397106 +- 4.239728 -2.765377 6.742145 +- 4.154910 -0.430195 8.968298 +- 4.588103 -1.686764 8.920565 +- 4.748481 -1.226887 9.884511 +- 5.030638 -2.930357 8.914329 +- 5.276823 -4.138026 8.363485 ++ 2.623224 0.684847 5.224690 ++ 2.631874 -0.707517 3.706295 ++ 2.874735 -1.252950 2.473241 ++ 2.981754 -0.611820 1.610746 ++ 3.015083 -2.545282 2.486669 ++ 2.854431 -2.887097 3.824373 ++ 2.890057 -4.114829 4.496241 ++ 3.109804 -5.286605 3.884480 ++ 3.124371 -6.141804 4.421623 ++ 3.260868 -5.314611 2.886234 ++ 2.691903 -4.099290 5.821417 ++ 2.474287 -2.933307 6.423105 ++ 2.312232 -2.898303 7.490303 ++ 2.418509 -1.722706 5.899909 ++ 2.621151 -1.767164 4.565946 + 2.575655 2.966926 3.331156 + 2.881929 3.535802 2.453274 + 3.424925 1.698847 3.438931 +@@ -394,21 +394,21 @@ + 0.391890 3.029890 3.571783 + 1.142222 1.169994 3.879663 + 2.468198 0.737932 4.147078 +- 3.422991 1.160472 4.460013 +- 1.821628 0.329290 5.472166 +- 3.045980 -0.266556 5.623252 +- 3.300321 -1.253530 5.266050 +- 3.400654 0.078938 6.868419 +- 3.596750 0.739775 8.200650 +- 2.627095 1.008594 8.619702 +- 4.106045 0.052544 8.876247 +- 4.199810 1.639079 8.075463 +- 3.886987 -1.267611 6.713863 +- 4.193797 -1.026107 7.880244 +- 4.182336 -2.491705 6.149271 +- 4.473391 -2.322796 7.186024 +- 4.489928 -3.724276 5.610241 +- 4.916436 -3.803915 6.750481 ++ 2.623224 0.684847 5.224690 ++ 2.632951 -0.717026 3.703395 ++ 2.875701 -1.078946 2.404555 ++ 2.959028 -0.321296 1.639425 ++ 3.067013 -2.361001 2.064944 ++ 3.333430 -2.767543 0.645879 ++ 4.242250 -2.280529 0.292378 ++ 3.457938 -3.849191 0.594530 ++ 2.493973 -2.468751 0.018077 ++ 3.022943 -3.401289 3.059659 ++ 3.186167 -4.600916 2.842510 ++ 2.773364 -2.946913 4.338586 ++ 2.730574 -3.698393 5.126967 ++ 2.572586 -1.635482 4.718372 ++ 2.357489 -1.330164 5.879800 + 2.575655 2.966926 3.331156 + 2.881929 3.535802 2.453274 + 3.424925 1.698847 3.438931 +@@ -612,22 +612,22 @@ + 0.391890 3.029890 3.571783 + 1.142222 1.169994 3.879663 + 2.468198 0.737932 4.147078 +- 3.422991 1.160472 4.460013 +- 1.809468 0.366314 5.430851 +- 2.985443 -0.303283 5.701265 +- 3.220128 -1.300453 5.359250 +- 3.217392 0.174542 6.898755 +- 3.501851 -1.098776 6.419335 +- 3.907092 -0.959542 7.773142 +- 4.306119 -2.122793 7.750193 +- 4.034999 -0.202628 8.943920 +- 4.092163 0.401223 9.738965 +- 4.527564 -1.484195 9.083085 +- 4.671337 -0.799117 10.225713 +- 4.406357 0.160408 10.396586 +- 5.109266 -1.288479 10.993073 +- 4.937775 -2.746085 8.992209 +- 5.203174 -3.983662 8.494648 ++ 2.623224 0.684847 5.224690 ++ 2.590680 -0.679098 3.703090 ++ 2.813126 -1.180187 2.436667 ++ 2.923918 -0.505423 1.600713 ++ 2.866567 -2.487992 2.382906 ++ 2.666616 -2.884782 3.699977 ++ 2.618169 -4.183246 4.272728 ++ 2.745111 -5.274676 3.719947 ++ 2.392358 -4.124071 5.653129 ++ 2.340242 -4.991533 6.147896 ++ 2.235991 -2.964895 6.385427 ++ 2.027971 -3.123388 7.699660 ++ 1.962797 -3.996113 8.203846 ++ 1.903765 -2.280234 8.241661 ++ 2.283795 -1.749407 5.847650 ++ 2.502701 -1.789347 4.505978 + 2.575655 2.966926 3.331156 + 2.881929 3.535802 2.453274 + 3.424925 1.698847 3.438931 +@@ -819,19 +819,19 @@ + 0.391890 3.029890 3.571783 + 1.142222 1.169994 3.879663 + 2.468198 0.737932 4.147078 +- 3.422991 1.160472 4.460013 +- 1.810222 0.365622 5.431037 +- 3.040503 -0.202936 5.543946 +- 3.303784 -1.184927 5.179558 +- 3.350889 0.129864 6.825549 +- 3.478253 0.640008 7.780343 +- 3.798907 -1.207335 6.588738 +- 4.083865 -0.848420 7.826630 +- 4.553596 -1.522140 8.414470 +- 3.834435 0.071716 8.160148 +- 4.146081 -2.428628 6.192742 +- 4.391834 -3.604440 5.555033 +- 4.829292 -3.701644 6.711226 ++ 2.623224 0.684847 5.224690 ++ 2.591673 -0.679108 3.703398 ++ 2.814053 -0.989708 2.398148 ++ 2.904088 -0.203069 1.663647 ++ 2.926420 -2.283840 1.995414 ++ 3.104659 -2.514231 0.945056 ++ 2.799915 -3.288854 3.004791 ++ 2.898410 -4.565463 2.683902 ++ 2.803322 -5.244627 3.425383 ++ 3.063325 -4.838262 1.725527 ++ 2.582464 -2.976080 4.279070 ++ 2.473124 -1.675585 4.661638 ++ 2.270623 -1.344205 5.839254 + 2.575655 2.966926 3.331156 + 2.881929 3.535802 2.453274 + 3.424925 1.698847 3.438931 +@@ -1043,21 +1043,21 @@ + 2.447108 3.477366 3.933855 + 3.228110 1.605160 3.977232 + 4.558604 1.150942 3.777549 +- 5.569373 1.557427 3.742678 +- 4.398936 0.755791 5.236576 +- 5.570721 0.053476 5.133763 +- 5.651435 -0.952100 4.748143 +- 6.248368 0.547472 6.127122 +- 6.337852 -0.727929 5.581736 +- 7.186443 -0.642297 6.691944 +- 7.489983 -1.917831 6.415398 +- 8.153280 -2.415516 6.991980 +- 7.055473 -2.381556 5.630375 +- 7.773936 -0.045280 7.737899 +- 8.144838 -1.308931 7.552106 +- 8.632452 -0.851805 8.400438 +- 8.538915 -2.559764 7.402037 +- 8.562807 -3.771388 6.807145 ++ 5.071990 1.095268 4.737463 ++ 4.538874 -0.297045 3.315659 ++ 4.336740 -0.846471 2.077041 ++ 4.152394 -0.207224 1.226289 ++ 4.452852 -2.140973 2.049069 ++ 4.754050 -2.480049 3.362997 ++ 4.997986 -3.708205 3.989198 ++ 4.976769 -4.883498 3.345899 ++ 5.160704 -5.738821 3.850568 ++ 4.776841 -4.914031 2.356355 ++ 5.265289 -3.689348 5.302131 ++ 5.284973 -2.519883 5.935270 ++ 5.498266 -2.482169 6.993326 ++ 5.072682 -1.308518 5.455764 ++ 4.806134 -1.356364 4.133205 + 4.415598 3.377823 2.961313 + 4.412064 3.941488 2.028377 + 5.230436 2.095693 2.779428 +@@ -1274,21 +1274,21 @@ + 2.447108 3.477366 3.933855 + 3.228110 1.605160 3.977232 + 4.558604 1.150942 3.777549 +- 5.569373 1.557427 3.742678 +- 4.397885 0.753191 5.246175 +- 5.590532 0.136915 4.972869 +- 5.691792 -0.854182 4.555888 +- 6.355081 0.476418 6.019675 +- 7.005380 1.133878 7.200716 +- 6.241886 1.418905 7.924551 +- 7.704141 0.438210 7.665344 +- 7.543334 2.022951 6.871696 +- 6.737960 -0.878090 5.715845 +- 7.428954 -0.641760 6.705579 +- 6.803084 -2.106960 5.091315 +- 7.433797 -1.942952 5.965044 +- 6.888321 -3.344512 4.486667 +- 7.677782 -3.431286 5.412745 ++ 5.071990 1.095268 4.737463 ++ 4.538744 -0.306572 3.312620 ++ 4.316895 -0.672508 2.011169 ++ 4.145425 0.083640 1.259346 ++ 4.360306 -1.957588 1.633963 ++ 4.118872 -2.368537 0.211701 ++ 4.859526 -1.896818 -0.434064 ++ 4.201263 -3.452119 0.127068 ++ 3.120134 -2.055722 -0.092882 ++ 4.642734 -2.996992 2.589722 ++ 4.702936 -4.199185 2.336724 ++ 4.852811 -2.538498 3.874265 ++ 5.070419 -3.289156 4.634040 ++ 4.814710 -1.223887 4.292292 ++ 5.014652 -0.915008 5.455485 + 4.415598 3.377823 2.961313 + 4.412064 3.941488 2.028377 + 5.230436 2.095693 2.779428 +@@ -1510,22 +1510,22 @@ + 2.447108 3.477366 3.933855 + 3.228110 1.605160 3.977232 + 4.558604 1.150942 3.777549 +- 5.569373 1.557427 3.742678 +- 4.372913 0.790414 5.211298 +- 5.559757 0.101208 5.067090 +- 5.647583 -0.899755 4.671160 +- 6.194776 0.575080 6.110305 +- 6.278024 -0.702826 5.569817 +- 7.123995 -0.570401 6.702600 +- 7.472741 -1.740173 6.551245 +- 7.656517 0.184264 7.754694 +- 7.991655 0.787072 8.478783 +- 8.146732 -1.105376 7.724367 +- 8.683403 -0.422802 8.744993 +- 8.507987 0.541027 8.990678 +- 9.349613 -0.919433 9.319121 +- 8.481202 -2.373962 7.505920 +- 8.540900 -3.615812 6.954699 ++ 5.071990 1.095268 4.737463 ++ 4.499521 -0.267941 3.326572 ++ 4.267491 -0.772686 2.063324 ++ 4.096298 -0.099873 1.236030 ++ 4.278725 -2.081203 2.002024 ++ 4.535077 -2.474587 3.310318 ++ 4.665007 -3.772057 3.872536 ++ 4.578030 -4.865461 3.315935 ++ 4.925900 -3.709107 5.246571 ++ 5.032497 -4.575574 5.734292 ++ 5.047695 -2.547474 5.981536 ++ 5.299246 -2.702459 7.288556 ++ 5.396714 -3.573970 7.789625 ++ 5.381197 -1.857343 7.835514 ++ 4.927816 -1.332957 5.452878 ++ 4.673984 -1.376560 4.117488 + 4.415598 3.377823 2.961313 + 4.412064 3.941488 2.028377 + 5.230436 2.095693 2.779428 +@@ -1735,19 +1735,19 @@ + 2.447108 3.477366 3.933855 + 3.228110 1.605160 3.977232 + 4.558604 1.150942 3.777549 +- 5.569373 1.557427 3.742678 +- 4.373674 0.789709 5.211219 +- 5.559264 0.200618 4.899855 +- 5.666544 -0.785646 4.473035 +- 6.294463 0.528171 5.996117 +- 6.748720 1.036110 6.846852 +- 6.613356 -0.816346 5.628040 +- 7.310127 -0.462256 6.691775 +- 7.941913 -1.143751 7.087389 +- 7.204329 0.461930 7.085204 +- 6.784882 -2.043285 5.144201 +- 6.779159 -3.223049 4.467648 +- 7.584089 -3.327568 5.405072 ++ 5.071990 1.095268 4.737463 ++ 4.500559 -0.267967 3.326521 ++ 4.258187 -0.582249 2.025720 ++ 4.103951 0.202771 1.300217 ++ 4.205645 -1.878082 1.616262 ++ 4.010240 -2.111427 0.569617 ++ 4.416190 -2.880836 2.613787 ++ 4.378882 -4.158916 2.285883 ++ 4.532450 -4.836391 3.019057 ++ 4.201751 -4.434440 1.330472 ++ 4.652634 -2.564463 3.883788 ++ 4.701224 -1.262318 4.273223 ++ 4.918947 -0.927591 5.447171 + 4.415598 3.377823 2.961313 + 4.412064 3.941488 2.028377 + 5.230436 2.095693 2.779428 +@@ -1953,27 +1953,27 @@ + 0.391890 3.029890 3.571783 + 1.142222 1.169994 3.879663 + 2.468198 0.737932 4.147078 +- 3.422991 1.160472 4.460013 +- 1.825854 0.331961 5.463505 +- 2.973744 -0.351218 5.767666 +- 3.198298 -1.353172 5.432908 +- 3.262456 0.147686 6.932887 +- 3.554407 -1.123002 6.450998 +- 3.970615 -1.030384 7.784487 +- 4.371751 -2.299375 7.628436 +- 4.806122 -2.789852 8.397106 +- 4.239728 -2.765377 6.742145 +- 4.154910 -0.430195 8.968298 +- 4.588103 -1.686764 8.920565 +- 4.748481 -1.226887 9.884511 +- 5.030638 -2.930357 8.914329 +- 5.276823 -4.138026 8.363485 ++ 2.623224 0.684847 5.224690 ++ 2.631874 -0.707517 3.706295 ++ 2.874735 -1.252950 2.473241 ++ 2.981754 -0.611820 1.610746 ++ 3.015083 -2.545282 2.486669 ++ 2.854431 -2.887097 3.824373 ++ 2.890057 -4.114829 4.496241 ++ 3.109804 -5.286605 3.884480 ++ 3.124371 -6.141804 4.421623 ++ 3.260868 -5.314611 2.886234 ++ 2.691903 -4.099290 5.821417 ++ 2.474287 -2.933307 6.423105 ++ 2.312232 -2.898303 7.490303 ++ 2.418509 -1.722706 5.899909 ++ 2.621151 -1.767164 4.565946 + 2.575655 2.966926 3.331156 + 2.881929 3.535802 2.453274 + 3.424925 1.698847 3.438931 + 4.177807 1.697081 2.650726 + 4.070872 1.663908 4.714248 +- 4.904136 2.139152 4.751846 ++ 4.591405 0.857803 4.743234 + 2.785622 3.721368 4.515694 + !entry.RA5.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x + 1 31 0 0 0 0 +@@ -2160,24 +2160,24 @@ + 0.391890 3.029890 3.571783 + 1.142222 1.169994 3.879663 + 2.468198 0.737932 4.147078 +- 3.422991 1.160472 4.460013 +- 1.821628 0.329290 5.472166 +- 3.045980 -0.266556 5.623252 +- 3.300321 -1.253530 5.266050 +- 3.400654 0.078938 6.868419 +- 3.529160 0.584527 7.825480 +- 3.886987 -1.267611 6.713863 +- 4.193797 -1.026107 7.880244 +- 4.182336 -2.491705 6.149271 +- 4.473391 -2.322796 7.186024 +- 4.489928 -3.724276 5.610241 +- 4.916436 -3.803915 6.750481 ++ 2.623224 0.684847 5.224690 ++ 2.632951 -0.717026 3.703395 ++ 2.875701 -1.078946 2.404555 ++ 2.959028 -0.321296 1.639425 ++ 3.067013 -2.361001 2.064944 ++ 3.258724 -2.626638 1.025337 ++ 3.022943 -3.401289 3.059659 ++ 3.186167 -4.600916 2.842510 ++ 2.773364 -2.946913 4.338586 ++ 2.730574 -3.698393 5.126967 ++ 2.572586 -1.635482 4.718372 ++ 2.357489 -1.330164 5.879800 + 2.575655 2.966926 3.331156 + 2.881929 3.535802 2.453274 + 3.424925 1.698847 3.438931 + 4.177807 1.697081 2.650726 + 4.070872 1.663908 4.714248 +- 4.904136 2.139152 4.751846 ++ 4.591405 0.857803 4.743234 + 2.785622 3.721368 4.515694 + !entry.RU5.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x + 1 28 0 0 0 0 +@@ -2378,28 +2378,28 @@ + 0.391890 3.029890 3.571783 + 1.142222 1.169994 3.879663 + 2.468198 0.737932 4.147078 +- 3.422991 1.160472 4.460013 +- 1.809468 0.366314 5.430851 +- 2.985443 -0.303283 5.701265 +- 3.220128 -1.300453 5.359250 +- 3.217392 0.174542 6.898755 +- 3.501851 -1.098776 6.419335 +- 3.907092 -0.959542 7.773142 +- 4.306119 -2.122793 7.750193 +- 4.034999 -0.202628 8.943920 +- 4.092163 0.401223 9.738965 +- 4.527564 -1.484195 9.083085 +- 4.671337 -0.799117 10.225713 +- 4.406357 0.160408 10.396586 +- 5.109266 -1.288479 10.993073 +- 4.937775 -2.746085 8.992209 +- 5.203174 -3.983662 8.494648 ++ 2.623224 0.684847 5.224690 ++ 2.590680 -0.679098 3.703090 ++ 2.813126 -1.180187 2.436667 ++ 2.923918 -0.505423 1.600713 ++ 2.866567 -2.487992 2.382906 ++ 2.666616 -2.884782 3.699977 ++ 2.618169 -4.183246 4.272728 ++ 2.745111 -5.274676 3.719947 ++ 2.392358 -4.124071 5.653129 ++ 2.340242 -4.991533 6.147896 ++ 2.235991 -2.964895 6.385427 ++ 2.027971 -3.123388 7.699660 ++ 1.962797 -3.996113 8.203846 ++ 1.903765 -2.280234 8.241661 ++ 2.283795 -1.749407 5.847650 ++ 2.502701 -1.789347 4.505978 + 2.575655 2.966926 3.331156 + 2.881929 3.535802 2.453274 + 3.424925 1.698847 3.438931 + 4.177807 1.697081 2.650726 + 4.070872 1.663908 4.714248 +- 4.904136 2.139152 4.751846 ++ 4.591405 0.857803 4.743234 + 2.785622 3.721368 4.515694 + !entry.RG5.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x + 1 32 0 0 0 0 +@@ -2591,25 +2591,25 @@ + 0.391890 3.029890 3.571783 + 1.142222 1.169994 3.879663 + 2.468198 0.737932 4.147078 +- 3.422991 1.160472 4.460013 +- 1.810222 0.365622 5.431037 +- 3.040503 -0.202936 5.543946 +- 3.303784 -1.184927 5.179558 +- 3.350889 0.129864 6.825549 +- 3.478253 0.640008 7.780343 +- 3.798907 -1.207335 6.588738 +- 4.083865 -0.848420 7.826630 +- 4.553596 -1.522140 8.414470 +- 3.834435 0.071716 8.160148 +- 4.146081 -2.428628 6.192742 +- 4.391834 -3.604440 5.555033 +- 4.829292 -3.701644 6.711226 ++ 2.623224 0.684847 5.224690 ++ 2.591673 -0.679108 3.703398 ++ 2.814053 -0.989708 2.398148 ++ 2.904088 -0.203069 1.663647 ++ 2.926420 -2.283840 1.995414 ++ 3.104659 -2.514231 0.945056 ++ 2.799915 -3.288854 3.004791 ++ 2.898410 -4.565463 2.683902 ++ 2.803322 -5.244627 3.425383 ++ 3.063325 -4.838262 1.725527 ++ 2.582464 -2.976080 4.279070 ++ 2.473124 -1.675585 4.661638 ++ 2.270623 -1.344205 5.839254 + 2.575655 2.966926 3.331156 + 2.881929 3.535802 2.453274 + 3.424925 1.698847 3.438931 + 4.177807 1.697081 2.650726 + 4.070872 1.663908 4.714248 +- 4.904136 2.139152 4.751846 ++ 4.591405 0.857803 4.743234 + 2.785622 3.721368 4.515694 + !entry.RC5.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x + 1 29 0 0 0 0 +@@ -2821,27 +2821,27 @@ + 2.447108 3.477366 3.933855 + 3.228110 1.605160 3.977232 + 4.558604 1.150942 3.777549 +- 5.569373 1.557427 3.742678 +- 4.398936 0.755791 5.236576 +- 5.570721 0.053476 5.133763 +- 5.651435 -0.952100 4.748143 +- 6.248368 0.547472 6.127122 +- 6.337852 -0.727929 5.581736 +- 7.186443 -0.642297 6.691944 +- 7.489983 -1.917831 6.415398 +- 8.153280 -2.415516 6.991980 +- 7.055473 -2.381556 5.630375 +- 7.773936 -0.045280 7.737899 +- 8.144838 -1.308931 7.552106 +- 8.632452 -0.851805 8.400438 +- 8.538915 -2.559764 7.402037 +- 8.562807 -3.771388 6.807145 ++ 5.071990 1.095268 4.737463 ++ 4.538874 -0.297045 3.315659 ++ 4.336740 -0.846471 2.077041 ++ 4.152394 -0.207224 1.226289 ++ 4.452852 -2.140973 2.049069 ++ 4.754050 -2.480049 3.362997 ++ 4.997986 -3.708205 3.989198 ++ 4.976769 -4.883498 3.345899 ++ 5.160704 -5.738821 3.850568 ++ 4.776841 -4.914031 2.356355 ++ 5.265289 -3.689348 5.302131 ++ 5.284973 -2.519883 5.935270 ++ 5.498266 -2.482169 6.993326 ++ 5.072682 -1.308518 5.455764 ++ 4.806134 -1.356364 4.133205 + 4.415598 3.377823 2.961313 + 4.412064 3.941488 2.028377 + 5.230436 2.095693 2.779428 + 5.668203 2.081314 1.781304 + 6.272975 2.049937 3.757138 +- 7.076220 2.511153 3.504793 ++ 6.759270 1.235224 3.610988 + 5.029888 4.128641 3.998289 + 5.911975 4.450154 3.797910 + !entry.RA3.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -3046,24 +3046,24 @@ + 2.447108 3.477366 3.933855 + 3.228110 1.605160 3.977232 + 4.558604 1.150942 3.777549 +- 5.569373 1.557427 3.742678 +- 4.397885 0.753191 5.246175 +- 5.590532 0.136915 4.972869 +- 5.691792 -0.854182 4.555888 +- 6.355081 0.476418 6.019675 +- 6.811115 0.979784 6.872175 +- 6.737960 -0.878090 5.715845 +- 7.428954 -0.641760 6.705579 +- 6.803084 -2.106960 5.091315 +- 7.433797 -1.942952 5.965044 +- 6.888321 -3.344512 4.486667 +- 7.677782 -3.431286 5.412745 ++ 5.071990 1.095268 4.737463 ++ 4.538744 -0.306572 3.312620 ++ 4.316895 -0.672508 2.011169 ++ 4.145425 0.083640 1.259346 ++ 4.360306 -1.957588 1.633963 ++ 4.180681 -2.226400 0.593014 ++ 4.642734 -2.996992 2.589722 ++ 4.702936 -4.199185 2.336724 ++ 4.852811 -2.538498 3.874265 ++ 5.070419 -3.289156 4.634040 ++ 4.814710 -1.223887 4.292292 ++ 5.014652 -0.915008 5.455485 + 4.415598 3.377823 2.961313 + 4.412064 3.941488 2.028377 + 5.230436 2.095693 2.779428 + 5.668203 2.081314 1.781304 + 6.272975 2.049937 3.757138 +- 7.076220 2.511153 3.504793 ++ 6.759270 1.235224 3.610988 + 5.029888 4.128641 3.998289 + 5.911975 4.450154 3.797910 + !entry.RU3.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -3282,28 +3282,28 @@ + 2.447108 3.477366 3.933855 + 3.228110 1.605160 3.977232 + 4.558604 1.150942 3.777549 +- 5.569373 1.557427 3.742678 +- 4.372913 0.790414 5.211298 +- 5.559757 0.101208 5.067090 +- 5.647583 -0.899755 4.671160 +- 6.194776 0.575080 6.110305 +- 6.278024 -0.702826 5.569817 +- 7.123995 -0.570401 6.702600 +- 7.472741 -1.740173 6.551245 +- 7.656517 0.184264 7.754694 +- 7.991655 0.787072 8.478783 +- 8.146732 -1.105376 7.724367 +- 8.683403 -0.422802 8.744993 +- 8.507987 0.541027 8.990678 +- 9.349613 -0.919433 9.319121 +- 8.481202 -2.373962 7.505920 +- 8.540900 -3.615812 6.954699 ++ 5.071990 1.095268 4.737463 ++ 4.499521 -0.267941 3.326572 ++ 4.267491 -0.772686 2.063324 ++ 4.096298 -0.099873 1.236030 ++ 4.278725 -2.081203 2.002024 ++ 4.535077 -2.474587 3.310318 ++ 4.665007 -3.772057 3.872536 ++ 4.578030 -4.865461 3.315935 ++ 4.925900 -3.709107 5.246571 ++ 5.032497 -4.575574 5.734292 ++ 5.047695 -2.547474 5.981536 ++ 5.299246 -2.702459 7.288556 ++ 5.396714 -3.573970 7.789625 ++ 5.381197 -1.857343 7.835514 ++ 4.927816 -1.332957 5.452878 ++ 4.673984 -1.376560 4.117488 + 4.415598 3.377823 2.961313 + 4.412064 3.941488 2.028377 + 5.230436 2.095693 2.779428 + 5.668203 2.081314 1.781304 + 6.272975 2.049937 3.757138 +- 7.076220 2.511153 3.504793 ++ 6.759270 1.235224 3.610988 + 5.029888 4.128641 3.998289 + 5.911975 4.450154 3.797910 + !entry.RG3.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -3513,25 +3513,25 @@ + 2.447108 3.477366 3.933855 + 3.228110 1.605160 3.977232 + 4.558604 1.150942 3.777549 +- 5.569373 1.557427 3.742678 +- 4.373674 0.789709 5.211219 +- 5.559264 0.200618 4.899855 +- 5.666544 -0.785646 4.473035 +- 6.294463 0.528171 5.996117 +- 6.748720 1.036110 6.846852 +- 6.613356 -0.816346 5.628040 +- 7.310127 -0.462256 6.691775 +- 7.941913 -1.143751 7.087389 +- 7.204329 0.461930 7.085204 +- 6.784882 -2.043285 5.144201 +- 6.779159 -3.223049 4.467648 +- 7.584089 -3.327568 5.405072 ++ 5.071990 1.095268 4.737463 ++ 4.500559 -0.267967 3.326521 ++ 4.258187 -0.582249 2.025720 ++ 4.103951 0.202771 1.300217 ++ 4.205645 -1.878082 1.616262 ++ 4.010240 -2.111427 0.569617 ++ 4.416190 -2.880836 2.613787 ++ 4.378882 -4.158916 2.285883 ++ 4.532450 -4.836391 3.019057 ++ 4.201751 -4.434440 1.330472 ++ 4.652634 -2.564463 3.883788 ++ 4.701224 -1.262318 4.273223 ++ 4.918947 -0.927591 5.447171 + 4.415598 3.377823 2.961313 + 4.412064 3.941488 2.028377 + 5.230436 2.095693 2.779428 + 5.668203 2.081314 1.781304 + 6.272975 2.049937 3.757138 +- 7.076220 2.511153 3.504793 ++ 6.759270 1.235224 3.610988 + 5.029888 4.128641 3.998289 + 5.911975 4.450154 3.797910 + !entry.RC3.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -3739,21 +3739,21 @@ + 2.447108 3.477366 3.933855 + 3.228110 1.605160 3.977232 + 4.558604 1.150942 3.777549 +- 5.569373 1.557427 3.742678 +- 4.398936 0.755791 5.236576 +- 5.570721 0.053476 5.133763 +- 5.651435 -0.952100 4.748143 +- 6.248368 0.547472 6.127122 +- 6.337852 -0.727929 5.581736 +- 7.186443 -0.642297 6.691944 +- 7.489983 -1.917831 6.415398 +- 8.153280 -2.415516 6.991980 +- 7.055473 -2.381556 5.630375 +- 7.773936 -0.045280 7.737899 +- 8.144838 -1.308931 7.552106 +- 8.632452 -0.851805 8.400438 +- 8.538915 -2.559764 7.402037 +- 8.562807 -3.771388 6.807145 ++ 5.071990 1.095268 4.737463 ++ 4.538874 -0.297045 3.315659 ++ 4.336740 -0.846471 2.077041 ++ 4.152394 -0.207224 1.226289 ++ 4.452852 -2.140973 2.049069 ++ 4.754050 -2.480049 3.362997 ++ 4.997986 -3.708205 3.989198 ++ 4.976769 -4.883498 3.345899 ++ 5.160704 -5.738821 3.850568 ++ 4.776841 -4.914031 2.356355 ++ 5.265289 -3.689348 5.302131 ++ 5.284973 -2.519883 5.935270 ++ 5.498266 -2.482169 6.993326 ++ 5.072682 -1.308518 5.455764 ++ 4.806134 -1.356364 4.133205 + 4.415598 3.377823 2.961313 + 4.412064 3.941488 2.028377 + 5.230436 2.095693 2.779428 +@@ -3964,21 +3964,21 @@ + 2.447108 3.477366 3.933855 + 3.228110 1.605160 3.977232 + 4.558604 1.150942 3.777549 +- 5.569373 1.557427 3.742678 +- 4.397885 0.753191 5.246175 +- 5.590532 0.136915 4.972869 +- 5.691792 -0.854182 4.555888 +- 6.355081 0.476418 6.019675 +- 7.005380 1.133878 7.200716 +- 6.241886 1.418905 7.924551 +- 7.704141 0.438210 7.665344 +- 7.543334 2.022951 6.871696 +- 6.737960 -0.878090 5.715845 +- 7.428954 -0.641760 6.705579 +- 6.803084 -2.106960 5.091315 +- 7.433797 -1.942952 5.965044 +- 6.888321 -3.344512 4.486667 +- 7.677782 -3.431286 5.412745 ++ 5.071990 1.095268 4.737463 ++ 4.538744 -0.306572 3.312620 ++ 4.316895 -0.672508 2.011169 ++ 4.145425 0.083640 1.259346 ++ 4.360306 -1.957588 1.633963 ++ 4.118872 -2.368537 0.211701 ++ 4.859526 -1.896818 -0.434064 ++ 4.201263 -3.452119 0.127068 ++ 3.120134 -2.055722 -0.092882 ++ 4.642734 -2.996992 2.589722 ++ 4.702936 -4.199185 2.336724 ++ 4.852811 -2.538498 3.874265 ++ 5.070419 -3.289156 4.634040 ++ 4.814710 -1.223887 4.292292 ++ 5.014652 -0.915008 5.455485 + 4.415598 3.377823 2.961313 + 4.412064 3.941488 2.028377 + 5.230436 2.095693 2.779428 +@@ -4194,22 +4194,22 @@ + 2.447108 3.477366 3.933855 + 3.228110 1.605160 3.977232 + 4.558604 1.150942 3.777549 +- 5.569373 1.557427 3.742678 +- 4.372913 0.790414 5.211298 +- 5.559757 0.101208 5.067090 +- 5.647583 -0.899755 4.671160 +- 6.194776 0.575080 6.110305 +- 6.278024 -0.702826 5.569817 +- 7.123995 -0.570401 6.702600 +- 7.472741 -1.740173 6.551245 +- 7.656517 0.184264 7.754694 +- 7.991655 0.787072 8.478783 +- 8.146732 -1.105376 7.724367 +- 8.683403 -0.422802 8.744993 +- 8.507987 0.541027 8.990678 +- 9.349613 -0.919433 9.319121 +- 8.481202 -2.373962 7.505920 +- 8.540900 -3.615812 6.954699 ++ 5.071990 1.095268 4.737463 ++ 4.499521 -0.267941 3.326572 ++ 4.267491 -0.772686 2.063324 ++ 4.096298 -0.099873 1.236030 ++ 4.278725 -2.081203 2.002024 ++ 4.535077 -2.474587 3.310318 ++ 4.665007 -3.772057 3.872536 ++ 4.578030 -4.865461 3.315935 ++ 4.925900 -3.709107 5.246571 ++ 5.032497 -4.575574 5.734292 ++ 5.047695 -2.547474 5.981536 ++ 5.299246 -2.702459 7.288556 ++ 5.396714 -3.573970 7.789625 ++ 5.381197 -1.857343 7.835514 ++ 4.927816 -1.332957 5.452878 ++ 4.673984 -1.376560 4.117488 + 4.415598 3.377823 2.961313 + 4.412064 3.941488 2.028377 + 5.230436 2.095693 2.779428 +@@ -4413,19 +4413,19 @@ + 2.447108 3.477366 3.933855 + 3.228110 1.605160 3.977232 + 4.558604 1.150942 3.777549 +- 5.569373 1.557427 3.742678 +- 4.373674 0.789709 5.211219 +- 5.559264 0.200618 4.899855 +- 5.666544 -0.785646 4.473035 +- 6.294463 0.528171 5.996117 +- 6.748720 1.036110 6.846852 +- 6.613356 -0.816346 5.628040 +- 7.310127 -0.462256 6.691775 +- 7.941913 -1.143751 7.087389 +- 7.204329 0.461930 7.085204 +- 6.784882 -2.043285 5.144201 +- 6.779159 -3.223049 4.467648 +- 7.584089 -3.327568 5.405072 ++ 5.071990 1.095268 4.737463 ++ 4.500559 -0.267967 3.326521 ++ 4.258187 -0.582249 2.025720 ++ 4.103951 0.202771 1.300217 ++ 4.205645 -1.878082 1.616262 ++ 4.010240 -2.111427 0.569617 ++ 4.416190 -2.880836 2.613787 ++ 4.378882 -4.158916 2.285883 ++ 4.532450 -4.836391 3.019057 ++ 4.201751 -4.434440 1.330472 ++ 4.652634 -2.564463 3.883788 ++ 4.701224 -1.262318 4.273223 ++ 4.918947 -0.927591 5.447171 + 4.415598 3.377823 2.961313 + 4.412064 3.941488 2.028377 + 5.230436 2.095693 2.779428 +@@ -4639,27 +4639,27 @@ + 2.447108 3.477366 3.933855 + 3.228110 1.605160 3.977232 + 4.558604 1.150942 3.777549 +- 5.569373 1.557427 3.742678 +- 4.398936 0.755791 5.236576 +- 5.570721 0.053476 5.133763 +- 5.651435 -0.952100 4.748143 +- 6.248368 0.547472 6.127122 +- 6.337852 -0.727929 5.581736 +- 7.186443 -0.642297 6.691944 +- 7.489983 -1.917831 6.415398 +- 8.153280 -2.415516 6.991980 +- 7.055473 -2.381556 5.630375 +- 7.773936 -0.045280 7.737899 +- 8.144838 -1.308931 7.552106 +- 8.632452 -0.851805 8.400438 +- 8.538915 -2.559764 7.402037 +- 8.562807 -3.771388 6.807145 ++ 5.071990 1.095268 4.737463 ++ 4.538874 -0.297045 3.315659 ++ 4.336740 -0.846471 2.077041 ++ 4.152394 -0.207224 1.226289 ++ 4.452852 -2.140973 2.049069 ++ 4.754050 -2.480049 3.362997 ++ 4.997986 -3.708205 3.989198 ++ 4.976769 -4.883498 3.345899 ++ 5.160704 -5.738821 3.850568 ++ 4.776841 -4.914031 2.356355 ++ 5.265289 -3.689348 5.302131 ++ 5.284973 -2.519883 5.935270 ++ 5.498266 -2.482169 6.993326 ++ 5.072682 -1.308518 5.455764 ++ 4.806134 -1.356364 4.133205 + 4.415598 3.377823 2.961313 + 4.412064 3.941488 2.028377 + 5.230436 2.095693 2.779428 + 5.668203 2.081314 1.781304 + 6.272975 2.049937 3.757138 +- 7.076220 2.511153 3.504793 ++ 6.759270 1.235224 3.610988 + 5.029888 4.128641 3.998289 + !entry.RA.unit.residueconnect table int c1x int c2x int c3x int c4x= int c5x int c6x + 1 33 0 0 0 0 +@@ -4858,24 +4858,24 @@ + 2.447108 3.477366 3.933855 + 3.228110 1.605160 3.977232 + 4.558604 1.150942 3.777549 +- 5.569373 1.557427 3.742678 +- 4.397885 0.753191 5.246175 +- 5.590532 0.136915 4.972869 +- 5.691792 -0.854182 4.555888 +- 6.355081 0.476418 6.019675 +- 6.811115 0.979784 6.872175 +- 6.737960 -0.878090 5.715845 +- 7.428954 -0.641760 6.705579 +- 6.803084 -2.106960 5.091315 +- 7.433797 -1.942952 5.965044 +- 6.888321 -3.344512 4.486667 +- 7.677782 -3.431286 5.412745 ++ 5.071990 1.095268 4.737463 ++ 4.538744 -0.306572 3.312620 ++ 4.316895 -0.672508 2.011169 ++ 4.145425 0.083640 1.259346 ++ 4.360306 -1.957588 1.633963 ++ 4.180681 -2.226400 0.593014 ++ 4.642734 -2.996992 2.589722 ++ 4.702936 -4.199185 2.336724 ++ 4.852811 -2.538498 3.874265 ++ 5.070419 -3.289156 4.634040 ++ 4.814710 -1.223887 4.292292 ++ 5.014652 -0.915008 5.455485 + 4.415598 3.377823 2.961313 + 4.412064 3.941488 2.028377 + 5.230436 2.095693 2.779428 + 5.668203 2.081314 1.781304 + 6.272975 2.049937 3.757138 +- 7.076220 2.511153 3.504793 ++ 6.759270 1.235224 3.610988 + 5.029888 4.128641 3.998289 + !entry.RU.unit.residueconnect table int c1x int c2x int c3x int c4x= int c5x int c6x + 1 30 0 0 0 0 +@@ -5088,28 +5088,28 @@ + 2.447108 3.477366 3.933855 + 3.228110 1.605160 3.977232 + 4.558604 1.150942 3.777549 +- 5.569373 1.557427 3.742678 +- 4.372913 0.790414 5.211298 +- 5.559757 0.101208 5.067090 +- 5.647583 -0.899755 4.671160 +- 6.194776 0.575080 6.110305 +- 6.278024 -0.702826 5.569817 +- 7.123995 -0.570401 6.702600 +- 7.472741 -1.740173 6.551245 +- 7.656517 0.184264 7.754694 +- 7.991655 0.787072 8.478783 +- 8.146732 -1.105376 7.724367 +- 8.683403 -0.422802 8.744993 +- 8.507987 0.541027 8.990678 +- 9.349613 -0.919433 9.319121 +- 8.481202 -2.373962 7.505920 +- 8.540900 -3.615812 6.954699 ++ 5.071990 1.095268 4.737463 ++ 4.499521 -0.267941 3.326572 ++ 4.267491 -0.772686 2.063324 ++ 4.096298 -0.099873 1.236030 ++ 4.278725 -2.081203 2.002024 ++ 4.535077 -2.474587 3.310318 ++ 4.665007 -3.772057 3.872536 ++ 4.578030 -4.865461 3.315935 ++ 4.925900 -3.709107 5.246571 ++ 5.032497 -4.575574 5.734292 ++ 5.047695 -2.547474 5.981536 ++ 5.299246 -2.702459 7.288556 ++ 5.396714 -3.573970 7.789625 ++ 5.381197 -1.857343 7.835514 ++ 4.927816 -1.332957 5.452878 ++ 4.673984 -1.376560 4.117488 + 4.415598 3.377823 2.961313 + 4.412064 3.941488 2.028377 + 5.230436 2.095693 2.779428 + 5.668203 2.081314 1.781304 + 6.272975 2.049937 3.757138 +- 7.076220 2.511153 3.504793 ++ 6.759270 1.235224 3.610988 + 5.029888 4.128641 3.998289 + !entry.RG.unit.residueconnect table int c1x int c2x int c3x int c4x= int c5x int c6x + 1 34 0 0 0 0 +@@ -5313,25 +5313,25 @@ + 2.447108 3.477366 3.933855 + 3.228110 1.605160 3.977232 + 4.558604 1.150942 3.777549 +- 5.569373 1.557427 3.742678 +- 4.373674 0.789709 5.211219 +- 5.559264 0.200618 4.899855 +- 5.666544 -0.785646 4.473035 +- 6.294463 0.528171 5.996117 +- 6.748720 1.036110 6.846852 +- 6.613356 -0.816346 5.628040 +- 7.310127 -0.462256 6.691775 +- 7.941913 -1.143751 7.087389 +- 7.204329 0.461930 7.085204 +- 6.784882 -2.043285 5.144201 +- 6.779159 -3.223049 4.467648 +- 7.584089 -3.327568 5.405072 ++ 5.071990 1.095268 4.737463 ++ 4.500559 -0.267967 3.326521 ++ 4.258187 -0.582249 2.025720 ++ 4.103951 0.202771 1.300217 ++ 4.205645 -1.878082 1.616262 ++ 4.010240 -2.111427 0.569617 ++ 4.416190 -2.880836 2.613787 ++ 4.378882 -4.158916 2.285883 ++ 4.532450 -4.836391 3.019057 ++ 4.201751 -4.434440 1.330472 ++ 4.652634 -2.564463 3.883788 ++ 4.701224 -1.262318 4.273223 ++ 4.918947 -0.927591 5.447171 + 4.415598 3.377823 2.961313 + 4.412064 3.941488 2.028377 + 5.230436 2.095693 2.779428 + 5.668203 2.081314 1.781304 + 6.272975 2.049937 3.757138 +- 7.076220 2.511153 3.504793 ++ 6.759270 1.235224 3.610988 + 5.029888 4.128641 3.998289 + !entry.RC.unit.residueconnect table int c1x int c2x int c3x int c4x= int c5x int c6x + 1 31 0 0 0 0 +@@ -5531,21 +5531,21 @@ + 0.391890 3.029890 3.571783 + 1.142222 1.169994 3.879663 + 2.468198 0.737932 4.147078 +- 3.422991 1.160472 4.460013 +- 1.825854 0.331961 5.463505 +- 2.973744 -0.351218 5.767666 +- 3.198298 -1.353172 5.432908 +- 3.262456 0.147686 6.932887 +- 3.554407 -1.123002 6.450998 +- 3.970615 -1.030384 7.784487 +- 4.371751 -2.299375 7.628436 +- 4.806122 -2.789852 8.397106 +- 4.239728 -2.765377 6.742145 +- 4.154910 -0.430195 8.968298 +- 4.588103 -1.686764 8.920565 +- 4.748481 -1.226887 9.884511 +- 5.030638 -2.930357 8.914329 +- 5.276823 -4.138026 8.363485 ++ 2.623224 0.684847 5.224690 ++ 2.631874 -0.707517 3.706295 ++ 2.874735 -1.252950 2.473241 ++ 2.981754 -0.611820 1.610746 ++ 3.015083 -2.545282 2.486669 ++ 2.854431 -2.887097 3.824373 ++ 2.890057 -4.114829 4.496241 ++ 3.109804 -5.286605 3.884480 ++ 3.124371 -6.141804 4.421623 ++ 3.260868 -5.314611 2.886234 ++ 2.691903 -4.099290 5.821417 ++ 2.474287 -2.933307 6.423105 ++ 2.312232 -2.898303 7.490303 ++ 2.418509 -1.722706 5.899909 ++ 2.621151 -1.767164 4.565946 + 2.575655 2.966926 3.331156 + 2.881929 3.535802 2.453274 + 3.424925 1.698847 3.438931 +@@ -5750,21 +5750,21 @@ + 0.391890 3.029890 3.571783 + 1.142222 1.169994 3.879663 + 2.468198 0.737932 4.147078 +- 3.422991 1.160472 4.460013 +- 1.821628 0.329290 5.472166 +- 3.045980 -0.266556 5.623252 +- 3.300321 -1.253530 5.266050 +- 3.400654 0.078938 6.868419 +- 3.596750 0.739775 8.200650 +- 2.627095 1.008594 8.619702 +- 4.106045 0.052544 8.876247 +- 4.199810 1.639079 8.075463 +- 3.886987 -1.267611 6.713863 +- 4.193797 -1.026107 7.880244 +- 4.182336 -2.491705 6.149271 +- 4.473391 -2.322796 7.186024 +- 4.489928 -3.724276 5.610241 +- 4.916436 -3.803915 6.750481 ++ 2.623224 0.684847 5.224690 ++ 2.632951 -0.717026 3.703395 ++ 2.875701 -1.078946 2.404555 ++ 2.959028 -0.321296 1.639425 ++ 3.067013 -2.361001 2.064944 ++ 3.333430 -2.767543 0.645879 ++ 4.242250 -2.280529 0.292378 ++ 3.457938 -3.849191 0.594530 ++ 2.493973 -2.468751 0.018077 ++ 3.022943 -3.401289 3.059659 ++ 3.186167 -4.600916 2.842510 ++ 2.773364 -2.946913 4.338586 ++ 2.730574 -3.698393 5.126967 ++ 2.572586 -1.635482 4.718372 ++ 2.357489 -1.330164 5.879800 + 2.575655 2.966926 3.331156 + 2.881929 3.535802 2.453274 + 3.424925 1.698847 3.438931 +@@ -5974,22 +5974,22 @@ + 0.391890 3.029890 3.571783 + 1.142222 1.169994 3.879663 + 2.468198 0.737932 4.147078 +- 3.422991 1.160472 4.460013 +- 1.809468 0.366314 5.430851 +- 2.985443 -0.303283 5.701265 +- 3.220128 -1.300453 5.359250 +- 3.217392 0.174542 6.898755 +- 3.501851 -1.098776 6.419335 +- 3.907092 -0.959542 7.773142 +- 4.306119 -2.122793 7.750193 +- 4.034999 -0.202628 8.943920 +- 4.092163 0.401223 9.738965 +- 4.527564 -1.484195 9.083085 +- 4.671337 -0.799117 10.225713 +- 4.406357 0.160408 10.396586 +- 5.109266 -1.288479 10.993073 +- 4.937775 -2.746085 8.992209 +- 5.203174 -3.983662 8.494648 ++ 2.623224 0.684847 5.224690 ++ 2.590680 -0.679098 3.703090 ++ 2.813126 -1.180187 2.436667 ++ 2.923918 -0.505423 1.600713 ++ 2.866567 -2.487992 2.382906 ++ 2.666616 -2.884782 3.699977 ++ 2.618169 -4.183246 4.272728 ++ 2.745111 -5.274676 3.719947 ++ 2.392358 -4.124071 5.653129 ++ 2.340242 -4.991533 6.147896 ++ 2.235991 -2.964895 6.385427 ++ 2.027971 -3.123388 7.699660 ++ 1.962797 -3.996113 8.203846 ++ 1.903765 -2.280234 8.241661 ++ 2.283795 -1.749407 5.847650 ++ 2.502701 -1.789347 4.505978 + 2.575655 2.966926 3.331156 + 2.881929 3.535802 2.453274 + 3.424925 1.698847 3.438931 +@@ -6187,19 +6187,19 @@ + 0.391890 3.029890 3.571783 + 1.142222 1.169994 3.879663 + 2.468198 0.737932 4.147078 +- 3.422991 1.160472 4.460013 +- 1.810222 0.365622 5.431037 +- 3.040503 -0.202936 5.543946 +- 3.303784 -1.184927 5.179558 +- 3.350889 0.129864 6.825549 +- 3.478253 0.640008 7.780343 +- 3.798907 -1.207335 6.588738 +- 4.083865 -0.848420 7.826630 +- 4.553596 -1.522140 8.414470 +- 3.834435 0.071716 8.160148 +- 4.146081 -2.428628 6.192742 +- 4.391834 -3.604440 5.555033 +- 4.829292 -3.701644 6.711226 ++ 2.623224 0.684847 5.224690 ++ 2.591673 -0.679108 3.703398 ++ 2.814053 -0.989708 2.398148 ++ 2.904088 -0.203069 1.663647 ++ 2.926420 -2.283840 1.995414 ++ 3.104659 -2.514231 0.945056 ++ 2.799915 -3.288854 3.004791 ++ 2.898410 -4.565463 2.683902 ++ 2.803322 -5.244627 3.425383 ++ 3.063325 -4.838262 1.725527 ++ 2.582464 -2.976080 4.279070 ++ 2.473124 -1.675585 4.661638 ++ 2.270623 -1.344205 5.839254 + 2.575655 2.966926 3.331156 + 2.881929 3.535802 2.453274 + 3.424925 1.698847 3.438931 +@@ -6407,27 +6407,27 @@ + 0.391890 3.029890 3.571783 + 1.142222 1.169994 3.879663 + 2.468198 0.737932 4.147078 +- 3.422991 1.160472 4.460013 +- 1.825854 0.331961 5.463505 +- 2.973744 -0.351218 5.767666 +- 3.198298 -1.353172 5.432908 +- 3.262456 0.147686 6.932887 +- 3.554407 -1.123002 6.450998 +- 3.970615 -1.030384 7.784487 +- 4.371751 -2.299375 7.628436 +- 4.806122 -2.789852 8.397106 +- 4.239728 -2.765377 6.742145 +- 4.154910 -0.430195 8.968298 +- 4.588103 -1.686764 8.920565 +- 4.748481 -1.226887 9.884511 +- 5.030638 -2.930357 8.914329 +- 5.276823 -4.138026 8.363485 ++ 2.623224 0.684847 5.224690 ++ 2.631874 -0.707517 3.706295 ++ 2.874735 -1.252950 2.473241 ++ 2.981754 -0.611820 1.610746 ++ 3.015083 -2.545282 2.486669 ++ 2.854431 -2.887097 3.824373 ++ 2.890057 -4.114829 4.496241 ++ 3.109804 -5.286605 3.884480 ++ 3.124371 -6.141804 4.421623 ++ 3.260868 -5.314611 2.886234 ++ 2.691903 -4.099290 5.821417 ++ 2.474287 -2.933307 6.423105 ++ 2.312232 -2.898303 7.490303 ++ 2.418509 -1.722706 5.899909 ++ 2.621151 -1.767164 4.565946 + 2.575655 2.966926 3.331156 + 2.881929 3.535802 2.453274 + 3.424925 1.698847 3.438931 + 4.177807 1.697081 2.650726 + 4.070872 1.663908 4.714248 +- 4.904136 2.139152 4.751846 ++ 4.591405 0.857803 4.743234 + 2.785622 3.721368 4.515694 + 3.677533 4.057871 4.629091 + !entry.RAN.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -6620,24 +6620,24 @@ + 0.391890 3.029890 3.571783 + 1.142222 1.169994 3.879663 + 2.468198 0.737932 4.147078 +- 3.422991 1.160472 4.460013 +- 1.821628 0.329290 5.472166 +- 3.045980 -0.266556 5.623252 +- 3.300321 -1.253530 5.266050 +- 3.400654 0.078938 6.868419 +- 3.529160 0.584527 7.825480 +- 3.886987 -1.267611 6.713863 +- 4.193797 -1.026107 7.880244 +- 4.182336 -2.491705 6.149271 +- 4.473391 -2.322796 7.186024 +- 4.489928 -3.724276 5.610241 +- 4.916436 -3.803915 6.750481 ++ 2.623224 0.684847 5.224690 ++ 2.632951 -0.717026 3.703395 ++ 2.875701 -1.078946 2.404555 ++ 2.959028 -0.321296 1.639425 ++ 3.067013 -2.361001 2.064944 ++ 3.258724 -2.626638 1.025337 ++ 3.022943 -3.401289 3.059659 ++ 3.186167 -4.600916 2.842510 ++ 2.773364 -2.946913 4.338586 ++ 2.730574 -3.698393 5.126967 ++ 2.572586 -1.635482 4.718372 ++ 2.357489 -1.330164 5.879800 + 2.575655 2.966926 3.331156 + 2.881929 3.535802 2.453274 + 3.424925 1.698847 3.438931 + 4.177807 1.697081 2.650726 + 4.070872 1.663908 4.714248 +- 4.904136 2.139152 4.751846 ++ 4.591405 0.857803 4.743234 + 2.785622 3.721368 4.515694 + 3.677533 4.057871 4.629091 + !entry.RUN.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -6844,28 +6844,28 @@ + 0.391890 3.029890 3.571783 + 1.142222 1.169994 3.879663 + 2.468198 0.737932 4.147078 +- 3.422991 1.160472 4.460013 +- 1.809468 0.366314 5.430851 +- 2.985443 -0.303283 5.701265 +- 3.220128 -1.300453 5.359250 +- 3.217392 0.174542 6.898755 +- 3.501851 -1.098776 6.419335 +- 3.907092 -0.959542 7.773142 +- 4.306119 -2.122793 7.750193 +- 4.034999 -0.202628 8.943920 +- 4.092163 0.401223 9.738965 +- 4.527564 -1.484195 9.083085 +- 4.671337 -0.799117 10.225713 +- 4.406357 0.160408 10.396586 +- 5.109266 -1.288479 10.993073 +- 4.937775 -2.746085 8.992209 +- 5.203174 -3.983662 8.494648 ++ 2.623224 0.684847 5.224690 ++ 2.590680 -0.679098 3.703090 ++ 2.813126 -1.180187 2.436667 ++ 2.923918 -0.505423 1.600713 ++ 2.866567 -2.487992 2.382906 ++ 2.666616 -2.884782 3.699977 ++ 2.618169 -4.183246 4.272728 ++ 2.745111 -5.274676 3.719947 ++ 2.392358 -4.124071 5.653129 ++ 2.340242 -4.991533 6.147896 ++ 2.235991 -2.964895 6.385427 ++ 2.027971 -3.123388 7.699660 ++ 1.962797 -3.996113 8.203846 ++ 1.903765 -2.280234 8.241661 ++ 2.283795 -1.749407 5.847650 ++ 2.502701 -1.789347 4.505978 + 2.575655 2.966926 3.331156 + 2.881929 3.535802 2.453274 + 3.424925 1.698847 3.438931 + 4.177807 1.697081 2.650726 + 4.070872 1.663908 4.714248 +- 4.904136 2.139152 4.751846 ++ 4.591405 0.857803 4.743234 + 2.785622 3.721368 4.515694 + 3.677533 4.057871 4.629091 + !entry.RGN.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +@@ -7063,25 +7063,25 @@ + 0.391890 3.029890 3.571783 + 1.142222 1.169994 3.879663 + 2.468198 0.737932 4.147078 +- 3.422991 1.160472 4.460013 +- 1.810222 0.365622 5.431037 +- 3.040503 -0.202936 5.543946 +- 3.303784 -1.184927 5.179558 +- 3.350889 0.129864 6.825549 +- 3.478253 0.640008 7.780343 +- 3.798907 -1.207335 6.588738 +- 4.083865 -0.848420 7.826630 +- 4.553596 -1.522140 8.414470 +- 3.834435 0.071716 8.160148 +- 4.146081 -2.428628 6.192742 +- 4.391834 -3.604440 5.555033 +- 4.829292 -3.701644 6.711226 ++ 2.623224 0.684847 5.224690 ++ 2.591673 -0.679108 3.703398 ++ 2.814053 -0.989708 2.398148 ++ 2.904088 -0.203069 1.663647 ++ 2.926420 -2.283840 1.995414 ++ 3.104659 -2.514231 0.945056 ++ 2.799915 -3.288854 3.004791 ++ 2.898410 -4.565463 2.683902 ++ 2.803322 -5.244627 3.425383 ++ 3.063325 -4.838262 1.725527 ++ 2.582464 -2.976080 4.279070 ++ 2.473124 -1.675585 4.661638 ++ 2.270623 -1.344205 5.839254 + 2.575655 2.966926 3.331156 + 2.881929 3.535802 2.453274 + 3.424925 1.698847 3.438931 + 4.177807 1.697081 2.650726 + 4.070872 1.663908 4.714248 +- 4.904136 2.139152 4.751846 ++ 4.591405 0.857803 4.743234 + 2.785622 3.721368 4.515694 + 3.677533 4.057871 4.629091 + !entry.RCN.unit.residueconnect table int c1x int c2x int c3x int c4= x int c5x int c6x +diff -urN amber11.orig/AmberTools/test/sqm/nma/nma.dftb.go.in amber11/Am= berTools/test/sqm/nma/nma.dftb.go.in +--- amber11.orig/AmberTools/test/sqm/nma/nma.dftb.go.in 1970-01-01 03:00= :00.000000000 +0300 ++++ amber11/AmberTools/test/sqm/nma/nma.dftb.go.in 2011-03-08 16:38:44.0= 00000000 +0300 +@@ -0,0 +1,30 @@ ++Run DFTB geometry optimization for NMA ++ &qmmm ++ qm_theory =3D 'DFTB', ++ qmcharge =3D 0, ++ ! SCF settings ++ scfconv =3D 1.0d-10, ! kcal/mol ++ errconv =3D 1.d-06, ! au ++ tight_p_conv =3D 0, ++ diag_routine =3D 1, ++ itrmax =3D 100, ++ ! Geometry optimization settings ++ maxcyc =3D 100, ++ grms_tol =3D 0.001, ! kcal/(mol*A) ++ ! Output ++ ntpr =3D 101, ++ verbosity =3D 0, ++ / ++ 6 C -0.767000 3.380000 4.245000 ++ 6 C -1.809707 2.570219 4.710852 ++ 7 N -2.661673 2.646098 3.869189 ++ 6 C -3.662846 1.855199 3.619926 ++ 8 O -1.634379 2.116691 5.584678 ++ 1 H 0.218271 3.164467 4.684075 ++ 1 H -0.578839 3.210298 3.174581 ++ 1 H -1.024346 4.421330 4.488732 ++ 1 H -2.569216 3.204198 3.074324 ++ 1 H -3.347225 0.824359 3.812610 ++ 1 H -4.529359 1.998602 4.311686 ++ 1 H -4.036138 1.906340 2.552627 ++ +diff -urN amber11.orig/AmberTools/test/sqm/nma/nma.dftb.go.out.save ambe= r11/AmberTools/test/sqm/nma/nma.dftb.go.out.save +--- amber11.orig/AmberTools/test/sqm/nma/nma.dftb.go.out.save 1970-01-01= 03:00:00.000000000 +0300 ++++ amber11/AmberTools/test/sqm/nma/nma.dftb.go.out.save 2011-03-08 16:3= 8:44.000000000 +0300 +@@ -0,0 +1,81 @@ ++ -------------------------------------------------------- ++ AMBER SQM VERSION 1.4 ++=20 ++ By ++ Ross C. Walker, Michael F. Crowley, Scott Brozell, ++ Tim Giese, Andreas W. Goetz and David A. Case ++=20 ++ -------------------------------------------------------- ++=20 ++ ++-----------------------------------------------------------------------= --------- ++ QM CALCULATION INFO ++-----------------------------------------------------------------------= --------- ++ ++| QMMM: Citation for AMBER QMMM Run: ++| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019= , 2008 ++ ++| QMMM: DFTB Calculation - Additional citation for AMBER DFTB QMMM Run: ++| QMMM: Seabra, G.M., Walker, R.C. et al., J. PHYS. CHEM. A., 111, 56= 55, (2007) ++ ++ ++QMMM: SINGLET STATE CALCULATION ++QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =3D 15 ++ ++| QMMM: *** SCF convergence criteria *** ++| QMMM: Energy change : 0.1D-09 kcal/mol ++| QMMM: Error matrix |FP-PF| : 0.1D-05 au ++| QMMM: Density matrix change : 0.5D-06 ++| QMMM: Maximum number of SCF cycles : 100 ++ DFTB: Number of atom types =3D 4 ++ ++ Parameter files: ++ TYP (AT) TYP (AT) SK integral FILE ++| 1 1 (C ) 1 (C ) /Users/andi/sources/amber/dat/slko/C-C.skf ++| 2 1 (C ) 2 (N ) /Users/andi/sources/amber/dat/slko/C-N.skf ++| 3 1 (C ) 3 (O ) /Users/andi/sources/amber/dat/slko/C-O.skf ++| 4 1 (C ) 4 (H ) /Users/andi/sources/amber/dat/slko/C-H.skf ++| 5 2 (N ) 1 (C ) /Users/andi/sources/amber/dat/slko/N-C.skf ++| 6 2 (N ) 2 (N ) /Users/andi/sources/amber/dat/slko/N-N.skf ++| 7 2 (N ) 3 (O ) /Users/andi/sources/amber/dat/slko/N-O.skf ++| 8 2 (N ) 4 (H ) /Users/andi/sources/amber/dat/slko/N-H.skf ++| 9 3 (O ) 1 (C ) /Users/andi/sources/amber/dat/slko/O-C.skf ++| 10 3 (O ) 2 (N ) /Users/andi/sources/amber/dat/slko/O-N.skf ++| 11 3 (O ) 3 (O ) /Users/andi/sources/amber/dat/slko/O-O.skf ++| 12 3 (O ) 4 (H ) /Users/andi/sources/amber/dat/slko/O-H.skf ++| 13 4 (H ) 1 (C ) /Users/andi/sources/amber/dat/slko/H-C.skf ++| 14 4 (H ) 2 (N ) /Users/andi/sources/amber/dat/slko/H-N.skf ++| 15 4 (H ) 3 (O ) /Users/andi/sources/amber/dat/slko/H-O.skf ++| 16 4 (H ) 4 (H ) /Users/andi/sources/amber/dat/slko/H-H.skf ++ ++-----------------------------------------------------------------------= --------- ++ RESULTS ++-----------------------------------------------------------------------= --------- ++ ++ ... geometry converged ! ++ ++ Heat of formation =3D -1220.84132946 kcal/mol ( -52.93965= 264 eV) ++ Total SCF energy =3D -8463.39103876 kcal/mol ( -367.00017= 513 eV) ++=20 ++ Atomic Charges for Step 1 : ++ Atom Element Mulliken Charge ++ 1 C -0.279 ++ 2 C 0.493 ++ 3 N -0.250 ++ 4 C -0.073 ++ 5 O -0.507 ++ 6 H 0.096 ++ 7 H 0.073 ++ 8 H 0.073 ++ 9 H 0.186 ++ 10 H 0.097 ++ 11 H 0.045 ++ 12 H 0.045 ++ Total Mulliken Charge =3D 0.000 ++=20 ++=20 ++ Final Structure ++ ++ ++ --------- Calculation Completed ---------- ++ +diff -urN amber11.orig/AmberTools/test/sqm/nma/nma.dftb.sp.in amber11/Am= berTools/test/sqm/nma/nma.dftb.sp.in +--- amber11.orig/AmberTools/test/sqm/nma/nma.dftb.sp.in 1970-01-01 03:00= :00.000000000 +0300 ++++ amber11/AmberTools/test/sqm/nma/nma.dftb.sp.in 2011-03-08 16:38:44.0= 00000000 +0300 +@@ -0,0 +1,30 @@ ++Run PM3 single point calculation for NMA ++ &qmmm ++ qm_theory =3D 'DFTB', ++ qmcharge =3D 0, ++ ! SCF settings ++ scfconv =3D 1.0d-10, ! kcal/mol ++ errconv =3D 1.d-06, ! au ++ tight_p_conv =3D 0, ++ diag_routine =3D 1, ++ itrmax =3D 100, ++ ! Geometry optimization settings ++ maxcyc =3D 0, ++ grms_tol =3D 0.02, ! kcal/(mol*A) ++ ! Output ++ ntpr =3D 10, ++ verbosity =3D 0, ++ / ++ 6 C -0.767000 3.380000 4.245000 ++ 6 C -1.809707 2.570219 4.710852 ++ 7 N -2.661673 2.646098 3.869189 ++ 6 C -3.662846 1.855199 3.619926 ++ 8 O -1.634379 2.116691 5.584678 ++ 1 H 0.218271 3.164467 4.684075 ++ 1 H -0.578839 3.210298 3.174581 ++ 1 H -1.024346 4.421330 4.488732 ++ 1 H -2.569216 3.204198 3.074324 ++ 1 H -3.347225 0.824359 3.812610 ++ 1 H -4.529359 1.998602 4.311686 ++ 1 H -4.036138 1.906340 2.552627 ++ +diff -urN amber11.orig/AmberTools/test/sqm/nma/nma.dftb.sp.out.save ambe= r11/AmberTools/test/sqm/nma/nma.dftb.sp.out.save +--- amber11.orig/AmberTools/test/sqm/nma/nma.dftb.sp.out.save 1970-01-01= 03:00:00.000000000 +0300 ++++ amber11/AmberTools/test/sqm/nma/nma.dftb.sp.out.save 2011-03-08 16:3= 8:44.000000000 +0300 +@@ -0,0 +1,111 @@ ++ -------------------------------------------------------- ++ AMBER SQM VERSION 1.4 ++=20 ++ By ++ Ross C. Walker, Michael F. Crowley, Scott Brozell, ++ Tim Giese, Andreas W. Goetz and David A. Case ++=20 ++ -------------------------------------------------------- ++=20 ++ ++-----------------------------------------------------------------------= --------- ++ QM CALCULATION INFO ++-----------------------------------------------------------------------= --------- ++ ++| QMMM: Citation for AMBER QMMM Run: ++| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019= , 2008 ++ ++| QMMM: DFTB Calculation - Additional citation for AMBER DFTB QMMM Run: ++| QMMM: Seabra, G.M., Walker, R.C. et al., J. PHYS. CHEM. A., 111, 56= 55, (2007) ++ ++ ++QMMM: SINGLET STATE CALCULATION ++QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =3D 15 ++ ++| QMMM: *** SCF convergence criteria *** ++| QMMM: Energy change : 0.1D-09 kcal/mol ++| QMMM: Error matrix |FP-PF| : 0.1D-05 au ++| QMMM: Density matrix change : 0.5D-06 ++| QMMM: Maximum number of SCF cycles : 100 ++ DFTB: Number of atom types =3D 4 ++ ++ Parameter files: ++ TYP (AT) TYP (AT) SK integral FILE ++| 1 1 (C ) 1 (C ) /Users/andi/sources/amber/dat/slko/C-C.skf ++| 2 1 (C ) 2 (N ) /Users/andi/sources/amber/dat/slko/C-N.skf ++| 3 1 (C ) 3 (O ) /Users/andi/sources/amber/dat/slko/C-O.skf ++| 4 1 (C ) 4 (H ) /Users/andi/sources/amber/dat/slko/C-H.skf ++| 5 2 (N ) 1 (C ) /Users/andi/sources/amber/dat/slko/N-C.skf ++| 6 2 (N ) 2 (N ) /Users/andi/sources/amber/dat/slko/N-N.skf ++| 7 2 (N ) 3 (O ) /Users/andi/sources/amber/dat/slko/N-O.skf ++| 8 2 (N ) 4 (H ) /Users/andi/sources/amber/dat/slko/N-H.skf ++| 9 3 (O ) 1 (C ) /Users/andi/sources/amber/dat/slko/O-C.skf ++| 10 3 (O ) 2 (N ) /Users/andi/sources/amber/dat/slko/O-N.skf ++| 11 3 (O ) 3 (O ) /Users/andi/sources/amber/dat/slko/O-O.skf ++| 12 3 (O ) 4 (H ) /Users/andi/sources/amber/dat/slko/O-H.skf ++| 13 4 (H ) 1 (C ) /Users/andi/sources/amber/dat/slko/H-C.skf ++| 14 4 (H ) 2 (N ) /Users/andi/sources/amber/dat/slko/H-N.skf ++| 15 4 (H ) 3 (O ) /Users/andi/sources/amber/dat/slko/H-O.skf ++| 16 4 (H ) 4 (H ) /Users/andi/sources/amber/dat/slko/H-H.skf ++ ++ QMMM: QM Region Cartesian Coordinates (*=3Dlink atom)=20 ++ QMMM: QM_NO. MM_NO. ATOM X Y Z ++ QMMM: 1 1 C -0.7670 3.3800 4.2450 ++ QMMM: 2 2 C -1.8097 2.5702 4.7109 ++ QMMM: 3 3 N -2.6617 2.6461 3.8692 ++ QMMM: 4 4 C -3.6628 1.8552 3.6199 ++ QMMM: 5 5 O -1.6344 2.1167 5.5847 ++ QMMM: 6 6 H 0.2183 3.1645 4.6841 ++ QMMM: 7 7 H -0.5788 3.2103 3.1746 ++ QMMM: 8 8 H -1.0243 4.4213 4.4887 ++ QMMM: 9 9 H -2.5692 3.2042 3.0743 ++ QMMM: 10 10 H -3.3472 0.8244 3.8126 ++ QMMM: 11 11 H -4.5294 1.9986 4.3117 ++ QMMM: 12 12 H -4.0361 1.9063 2.5526 ++ ++-----------------------------------------------------------------------= --------- ++ RESULTS ++-----------------------------------------------------------------------= --------- ++ ++ ++ Heat of formation =3D -1039.27301701 kcal/mol ( -45.06625= 979 eV) ++ Total SCF energy =3D -8281.82272631 kcal/mol ( -359.12678= 229 eV) ++ Electronic energy =3D -8895.69306749 kcal/mol ( -385.74619= 780 eV) ++ Core-core repulsion =3D 613.87034117 kcal/mol ( 26.61941= 551 eV) ++=20 ++ Atomic Charges for Step 1 : ++ Atom Element Mulliken Charge ++ 1 C -0.347 ++ 2 C 0.560 ++ 3 N -0.202 ++ 4 C -0.066 ++ 5 O -0.439 ++ 6 H 0.077 ++ 7 H 0.048 ++ 8 H 0.072 ++ 9 H 0.187 ++ 10 H 0.044 ++ 11 H 0.029 ++ 12 H 0.037 ++ Total Mulliken Charge =3D 0.000 ++=20 ++=20 ++ Final Structure ++ ++ QMMM: QM Region Cartesian Coordinates (*=3Dlink atom)=20 ++ QMMM: QM_NO. MM_NO. ATOM X Y Z ++ QMMM: 1 1 C -0.7670 3.3800 4.2450 ++ QMMM: 2 2 C -1.8097 2.5702 4.7109 ++ QMMM: 3 3 N -2.6617 2.6461 3.8692 ++ QMMM: 4 4 C -3.6628 1.8552 3.6199 ++ QMMM: 5 5 O -1.6344 2.1167 5.5847 ++ QMMM: 6 6 H 0.2183 3.1645 4.6841 ++ QMMM: 7 7 H -0.5788 3.2103 3.1746 ++ QMMM: 8 8 H -1.0243 4.4213 4.4887 ++ QMMM: 9 9 H -2.5692 3.2042 3.0743 ++ QMMM: 10 10 H -3.3472 0.8244 3.8126 ++ QMMM: 11 11 H -4.5294 1.9986 4.3117 ++ QMMM: 12 12 H -4.0361 1.9063 2.5526 ++ ++ --------- Calculation Completed ---------- ++ +diff -urN amber11.orig/AmberTools/test/sqm/nma/Run amber11/AmberTools/te= st/sqm/nma/Run +--- amber11.orig/AmberTools/test/sqm/nma/Run 2010-04-14 17:26:17.0000000= 00 +0400 ++++ amber11/AmberTools/test/sqm/nma/Run 2011-03-08 16:38:44.000000000 +0= 300 +@@ -3,8 +3,19 @@ + set SQM =3D ../../../exe/sqm + set SPDIFF =3D ../../dacdif + set GODIFF =3D "../../dacdif -a 0.01" +-set SPTESTS =3D (nma.pm3.sp nma.pm6.sp) +-set GOTESTS =3D (nma.pm3.go nma.pm6.go) ++ ++# check if slko files for DFTB are installed ++../../check_slko_files.x ++if( $status > 0) then ++ # no slko files - do not run DFTB tests ++ set SPTESTS =3D (nma.pm3.sp nma.pm6.sp) ++ set GOTESTS =3D (nma.pm3.go nma.pm6.go) ++else ++ # slko files present - run DFTB tests ++ set SPTESTS =3D (nma.pm3.sp nma.pm6.sp nma.dftb.sp) ++ set GOTESTS =3D (nma.pm3.go nma.pm6.go nma.dftb.go) ++endif ++ +=20 + # single point tests + foreach i ($SPTESTS) +diff -urN amber11.orig/dat/leap/lib/amoeba_aminoct.off amber11/dat/leap/= lib/amoeba_aminoct.off +--- amber11.orig/dat/leap/lib/amoeba_aminoct.off 2010-03-31 07:05:27.000= 000000 +0400 ++++ amber11/dat/leap/lib/amoeba_aminoct.off 2011-03-08 16:38:44.00000000= 0 +0300 +@@ -638,24 +638,24 @@ + !entry.CCYX.unit.atoms table str name str type int typex int resx = int flags int seq int elmnt dbl chg str + "N" "7" 0 1 131072 1 7 -0.382100=20 + "H" "10" 0 1 131072 2 1 0.268100=20 +- "CA" "8" 0 1 131072 3 6 -0.131800=20 ++ "CA" "44" 0 1 131072 3 6 -0.131800=20 + "HA" "12" 0 1 131072 4 1 0.093800=20 +- "CB" "" 0 1 131072 5 6 -0.194300=20 +- "HB2" "" 0 1 131072 6 1 0.122800=20 +- "HB3" "" 0 1 131072 7 1 0.122800=20 +- "SG" "" 0 1 131072 8 16 -0.052900=20 ++ "CB" "45" 0 1 131072 5 6 -0.194300=20 ++ "HB2" "46" 0 1 131072 6 1 0.122800=20 ++ "HB3" "46" 0 1 131072 7 1 0.122800=20 ++ "SG" "49" 0 1 131072 8 16 -0.052900=20 + "C" "192" 0 1 131072 9 6 0.761800=20 + "O" "193" 0 1 131072 10 8 -0.804100=20 + "OXT" "193" 0 1 131072 11 8 -0.804100=20 + !entry.CCYX.unit.atomspertinfo table str pname str ptype int ptypex = int pelmnt dbl pchg + "N" "7" 0 -1 0.0 + "H" "10" 0 -1 0.0 +- "CA" "8" 0 -1 0.0 ++ "CA" "44" 0 -1 0.0 + "HA" "12" 0 -1 0.0 +- "CB" "" 0 -1 0.0 +- "HB2" "" 0 -1 0.0 +- "HB3" "" 0 -1 0.0 +- "SG" "" 0 -1 0.0 ++ "CB" "45" 0 -1 0.0 ++ "HB2" "46" 0 -1 0.0 ++ "HB3" "46" 0 -1 0.0 ++ "SG" "49" 0 -1 0.0 + "C" "192" 0 -1 0.0 + "O" "193" 0 -1 0.0 + "OXT" "193" 0 -1 0.0 +diff -urN amber11.orig/dat/leap/lib/amoeba_aminont.off amber11/dat/leap/= lib/amoeba_aminont.off +--- amber11.orig/dat/leap/lib/amoeba_aminont.off 2010-03-31 07:05:27.000= 000000 +0400 ++++ amber11/dat/leap/lib/amoeba_aminont.off 2011-03-08 16:38:44.00000000= 0 +0300 +@@ -736,12 +736,12 @@ + "H1" "191" 0 1 131072 2 1 0.181500=20 + "H2" "191" 0 1 131072 3 1 0.181500=20 + "H3" "191" 0 1 131072 4 1 0.181500=20 +- "CA" "8" 0 1 131072 5 6 0.105500=20 ++ "CA" "44" 0 1 131072 5 6 0.105500=20 + "HA" "12" 0 1 131072 6 1 0.092200=20 +- "CB" "" 0 1 131072 7 6 -0.027700=20 +- "HB2" "" 0 1 131072 8 1 0.068000=20 +- "HB3" "" 0 1 131072 9 1 0.068000=20 +- "SG" "" 0 1 131072 10 16 -0.098400=20 ++ "CB" "45" 0 1 131072 7 6 -0.027700=20 ++ "HB2" "46" 0 1 131072 8 1 0.068000=20 ++ "HB3" "46" 0 1 131072 9 1 0.068000=20 ++ "SG" "49" 0 1 131072 10 16 -0.098400=20 + "C" "9" 0 1 131072 11 6 0.612300=20 + "O" "11" 0 1 131072 12 8 -0.571300=20 + !entry.NCYX.unit.atomspertinfo table str pname str ptype int ptypex = int pelmnt dbl pchg +diff -urN amber11.orig/dat/leap/lib/amoeba_amino.off amber11/dat/leap/li= b/amoeba_amino.off +--- amber11.orig/dat/leap/lib/amoeba_amino.off 2010-03-31 07:05:27.00000= 0000 +0400 ++++ amber11/dat/leap/lib/amoeba_amino.off 2011-03-08 16:38:44.000000000 = +0300 +@@ -880,23 +880,23 @@ + !entry.CYX.unit.atoms table str name str type int typex int resx i= nt flags int seq int elmnt dbl chg str + "N" "7" 0 1 131072 1 7 -0.435921=20 + "H" "10" 0 1 131072 2 1 0.290077=20 +- "CA" "8" 0 1 131072 3 6 -0.030547=20 ++ "CA" "44" 0 1 131072 3 6 -0.030547=20 + "HA" "12" 0 1 131072 4 1 0.132146=20 +- "CB" "" 0 1 131072 5 6 -0.033006=20 +- "HB2" "" 0 1 131072 6 1 0.078951=20 +- "HB3" "" 0 1 131072 7 1 0.078951=20 +- "SG" "" 0 1 131072 8 16 -0.132272=20 ++ "CB" "45" 0 1 131072 5 6 -0.033006=20 ++ "HB2" "46" 0 1 131072 6 1 0.078951=20 ++ "HB3" "46" 0 1 131072 7 1 0.078951=20 ++ "SG" "49" 0 1 131072 8 16 -0.132272=20 + "C" "9" 0 1 131072 9 6 0.624788=20 + "O" "11" 0 1 131072 10 8 -0.573167=20 + !entry.CYX.unit.atomspertinfo table str pname str ptype int ptypex = int pelmnt dbl pchg + "N" "7" 0 -1 0.0 + "H" "10" 0 -1 0.0 +- "CA" "8" 0 -1 0.0 ++ "CA" "44" 0 -1 0.0 + "HA" "12" 0 -1 0.0 +- "CB" "" 0 -1 0.0 +- "HB2" "" 0 -1 0.0 +- "HB3" "" 0 -1 0.0 +- "SG" "" 0 -1 0.0 ++ "CB" "45" 0 -1 0.0 ++ "HB2" "46" 0 -1 0.0 ++ "HB3" "46" 0 -1 0.0 ++ "SG" "49" 0 -1 0.0 + "C" "9" 0 -1 0.0 + "O" "11" 0 -1 0.0 + !entry.CYX.unit.boundbox array dbl +@@ -990,16 +990,16 @@ + "H" "10" 0 -1 0.0 + "CA" "8" 0 -1 0.0 + "HA" "12" 0 -1 0.0 +- "CB" "" 0 -1 0.0 +- "HB2" "" 0 -1 0.0 +- "HB3" "" 0 -1 0.0 +- "CG" "" 0 -1 0.0 +- "HG2" "" 0 -1 0.0 +- "HG3" "" 0 -1 0.0 +- "CD" "" 0 -1 0.0 +- "OE1" "" 0 -1 0.0 +- "OE2" "" 0 -1 0.0 +- "HE2" "" 0 -1 0.0 ++ "CB" "144" 0 -1 0.0 ++ "HB2" "145" 0 -1 0.0 ++ "HB3" "145" 0 -1 0.0 ++ "CG" "146" 0 -1 0.0 ++ "HG2" "147" 0 -1 0.0 ++ "HG3" "147" 0 -1 0.0 ++ "CD" "148" 0 -1 0.0 ++ "OE1" "149" 0 -1 0.0 ++ "OE2" "149" 0 -1 0.0 ++ "HE2" "10" 0 -1 0.0 + "C" "9" 0 -1 0.0 + "O" "11" 0 -1 0.0 + !entry.GLH.unit.boundbox array dbl +@@ -2147,21 +2147,21 @@ + "H" "10" 0 -1 0.0 + "CA" "8" 0 -1 0.0 + "HA" "12" 0 -1 0.0 +- "CB" "" 0 -1 0.0 +- "HB2" "" 0 -1 0.0 +- "HB3" "" 0 -1 0.0 +- "CG" "" 0 -1 0.0 +- "HG2" "" 0 -1 0.0 +- "HG3" "" 0 -1 0.0 +- "CD" "" 0 -1 0.0 +- "HD2" "" 0 -1 0.0 +- "HD3" "" 0 -1 0.0 +- "CE" "" 0 -1 0.0 +- "HE2" "" 0 -1 0.0 +- "HE3" "" 0 -1 0.0 +- "NZ" "" 0 -1 0.0 +- "HZ2" "" 0 -1 0.0 +- "HZ3" "" 0 -1 0.0 ++ "CB" "159" 0 -1 0.0 ++ "HB2" "160" 0 -1 0.0 ++ "HB3" "160" 0 -1 0.0 ++ "CG" "161" 0 -1 0.0 ++ "HG2" "162" 0 -1 0.0 ++ "HG3" "162" 0 -1 0.0 ++ "CD" "163" 0 -1 0.0 ++ "HD2" "164" 0 -1 0.0 ++ "HD3" "164" 0 -1 0.0 ++ "CE" "165" 0 -1 0.0 ++ "HE2" "166" 0 -1 0.0 ++ "HE3" "166" 0 -1 0.0 ++ "NZ" "167" 0 -1 0.0 ++ "HZ2" "168" 0 -1 0.0 ++ "HZ3" "168" 0 -1 0.0 + "C" "9" 0 -1 0.0 + "O" "11" 0 -1 0.0 + !entry.LYN.unit.boundbox array dbl +diff -urN amber11.orig/dat/leap/parm/gaff.dat amber11/dat/leap/parm/gaff= .dat +--- amber11.orig/dat/leap/parm/gaff.dat 2010-03-31 07:05:27.000000000 +0= 400 ++++ amber11/dat/leap/parm/gaff.dat 2011-03-08 16:38:44.000000000 +0300 +@@ -16,6 +16,7 @@ + cy 12.01 0.360 Sp3 carbons in square systems + cu 12.01 0.360 Sp2 carbons in triangle systems + cv 12.01 0.360 Sp2 carbons in square systems ++cz 12.01 0.360 Sp2 carbon in guanidine group + h1 1.008 0.135 H bonded to aliphatic carbon with = 1 electrwd. group =20 + h2 1.008 0.135 H bonded to aliphatic carbon with = 2 electrwd. group=20 + h3 1.008 0.135 H bonded to aliphatic carbon with = 3 electrwd. group=20 +@@ -852,11 +853,6 @@ + s6-ss 139.6 2.1180 SOURCE3 5 0.0209 + sh-sh 158.9 2.0580 SOURCE2 1 0.0000 + sh-ss 155.8 2.0670 SOURCE3 3 0.0029 +-Si-c3 189.8 1.8928 SOURCE4 77 0.0061 +-Si-ca 191.1 1.8898 SOURCE4 11 0.0028 +-Si-ha 186.3 1.4887 SOURCE4 6 0.0040 +-Si-oh 267.6 1.6792 SOURCE4 6 0.0035 +-Si-os 287.7 1.6524 SOURCE4 22 0.0057 + s -s 169.0 2.0300 SOURCE3 1 0.0000 + s -s2 229.2 1.8970 SOURCE1 5 0.0000 + s -s4 152.8 2.0760 SOURCE3 4 0.0345 +@@ -1091,7 +1087,6 @@ + hc-c2-s6 54.150 115.450 SOURCE3 1=09 + hc-c2-sh 53.550 115.630 SOURCE3 1=09 + hc-c2-ss 54.900 115.620 SOURCE3 1=09 +-hn-c2-n4 0.000 112.740 SOURCE3 1=09 + hx-c2-n4 48.420 113.030 SOURCE3 3 0.3873 + i -c2-i 60.960 117.940 SOURCE3 1 0.0000 + n1-c2-n1 73.610 124.150 HF/6-31G* 1=09 +@@ -1464,9 +1459,6 @@ + s6-c3-s6 102.050 111.750 SOURCE3 1 0.0000 + sh-c3-sh 97.420 116.260 SOURCE3 1 0.0000 + sh-c3-ss 99.850 110.730 SOURCE3 1=09 +-Si-c3-c3 74.610 114.340 SOURCE4 26 1.1613 +-Si-c3-h1 51.040 110.900 SOURCE4 17 1.0270 +-Si-c3-hc 50.960 111.210 SOURCE4 222 0.4865 + s -c3-s 93.400 123.350 SOURCE3 1 0.0000 + ss-c3-ss 99.950 110.570 SOURCE4 15 1.4311 + br-ca-br 67.310 117.600 SOURCE3 1=09 +@@ -1500,7 +1492,6 @@ + ca-ca-i 58.590 118.470 SOURCE3 10 0.6181 + ca-ca-n1 68.920 118.500 HF/6-31G* 1=09 + ca-ca-n2 70.950 119.570 SOURCE3 1=09 +-ca-ca-n3 0.000 121.190 SOURCE3 1=09 + ca-ca-n4 67.280 118.410 SOURCE3 6 0.1691 + ca-ca-n 67.970 119.890 SOURCE3 18 0.2095 + ca-ca-na 70.210 118.340 SOURCE3 54 3.6168 +@@ -1540,7 +1531,6 @@ + cf-ca-nb 68.080 118.140 SOURCE4 12 1.1775 + cg-ca-cp 65.330 121.530 SOURCE4 12 0.1831 + c -ca-ha 46.510 115.900 SOURCE3 1=09 +-c -ca-hc 0.000 120.000 SOURCE3 1=09 + cl-ca-cl 62.630 118.720 SOURCE3 1=09 + cl-ca-cp 62.600 120.310 SOURCE4 18 0.5607 + cl-ca-nb 65.810 116.150 SOURCE4 50 0.6047 +@@ -1606,7 +1596,6 @@ + s4-ca-s4 104.060 105.810 SOURCE3 1=09 + s6-ca-s6 105.770 105.810 SOURCE3 1=09 + sh-ca-sh 98.150 120.240 SOURCE3 1=09 +-Si-ca-ca 73.850 121.430 SOURCE4 19 0.4235 + s -ca-s 98.380 125.140 SOURCE3 1=09 + ss-ca-ss 100.760 115.150 SOURCE3 1=09 + br-c -br 66.910 113.100 SOURCE3 1=09 +@@ -1636,7 +1625,6 @@ + c3-c -n 67.860 115.150 SOURCE3 153 2.7443 + c3-c -ne 68.090 111.390 SOURCE4 11 2.1430 + c3-c -nf 67.430 113.380 SOURCE3 1 same_as_c3-c-ne +-c3-c -nh 0.000 113.580 SOURCE3 1=09 + c3-c -o 68.030 123.110 SOURCE3 267 3.0977 + c3-c -oh 69.840 112.200 SOURCE3 14 1.8324 + c3-c -os 69.260 111.960 SOURCE3 15 2.3072 +@@ -1832,7 +1820,6 @@ + ha-cc-os 52.490 110.860 SOURCE3 7 1.3846 + ha-cc-pd 42.350 121.760 SOURCE3 84 same_as_ha-cd-pc + ha-cc-ss 53.490 121.640 SOURCE2 5 1.3276 +-c -c -hc 0.000 117.080 SOURCE3 1=09 + ch-c -ch 65.440 115.380 SOURCE3 1 same_as_cg-c-cg + ch-c -ha 47.800 113.900 SOURCE2 1 same_as_cg-c-ha + ch-c -o 70.210 122.310 SOURCE3 2 same_as_cg-c-o +@@ -2183,7 +2170,6 @@ + c -cf-n 66.600 116.790 SOURCE4 8 0.8255 + c -cf-nh 65.940 122.760 SOURCE3 1 same_as_c-ce-nh + f -c -f 72.220 107.350 SOURCE2 2 0.2500 +-f -c -h 0.000 109.900 SOURCE2 1 0.0000 + h4-cf-n2 52.210 122.140 SOURCE4 11 0.9297 + h4-cf-ne 52.280 120.210 SOURCE4 6 0.8104 + ha-cf-n1 52.480 115.960 SOURCE3 2 3.5425 +@@ -2239,34 +2225,20 @@ + cf-ch-cg 57.400 177.900 SOURCE4 8 0.4883 + cf-ch-n1 59.370 178.120 SOURCE4 22 1.5200 + cg-ch-ch 58.680 179.670 SOURCE4 7 0.1439 +-hc-c -hc 0.000 115.680 SOURCE3 1=09 +-hc-c -n 0.000 120.000 SOURCE3 1=09 +-hc-c -nh 0.000 112.700 SOURCE3 1=09 +-hc-c -o 0.000 120.000 SOURCE3 1=09 +-hc-c -oh 0.000 113.700 SOURCE3 1=09 +-hc-c -os 0.000 113.580 SOURCE3 1=09 + n1-ch-nf 64.660 176.170 SOURCE2 3 same_as_n1-cg-ne +-h -c -o 0.000 127.300 SOURCE2 1 0.0000 + i -c -i 59.790 116.450 SOURCE3 1 0.0000 + i -c -o 55.510 122.020 SOURCE3 4 1.2961 + f -cl-f 50.000 87.500 SOURCE2 1 estimated_force_cons= tant + n2-c -n2 71.830 110.310 SOURCE3 1=09 +-n2-c -na 0.000 118.600 SOURCE3 1=09 + n2-c -o 73.020 122.500 SOURCE3 1=09 +-n3-c -n3 0.000 112.980 SOURCE3 1=09 +-n3-c -o 0.000 122.260 SOURCE3 1=09 + n4-c -n4 64.710 114.640 SOURCE3 1 0.0000 + n4-c -o 69.580 118.830 SOURCE3 4 3.8516 +-na-c -na 0.000 115.400 SOURCE3 1=09 +-na-c -o 0.000 122.850 SOURCE3 1=09 + nc-c -o 74.050 123.980 SOURCE4 66 0.9502 + nd-c -o 73.720 121.760 SOURCE4 55 1.1138 + ne-c -ne 73.220 110.310 SOURCE3 1 0.0000 + ne-c -o 72.940 126.030 SOURCE4 39 0.9885 + nf-c -nf 73.070 110.310 SOURCE3 1 same_as_ne-c-ne + nf-c -o 73.320 124.390 SOURCE3 3 same_as_ne-c-o +-nh-c -nh 0.000 110.980 SOURCE3 1=09 +-nh-c -o 0.000 124.620 SOURCE3 1=09 + n -c -n 74.800 113.380 SOURCE4 635 1.4358 + n -c -nc 72.690 117.050 SOURCE4 54 0.7020 + n -c -nd 71.900 117.060 SOURCE4 23 0.9856 +@@ -2318,10 +2290,10 @@ + py-c -py 57.520 123.800 SOURCE3 1 0.0000 + ca-cq-ca 67.000 118.240 SOURCE4 5 0.2181 + ca-cq-cq 64.220 120.410 SOURCE4 12 1.4029 +-ca-cq-nb 0.000 122.970 SOURCE3 2 0.0000 ++ca-cq-nb 69.270 121.650 SOURCE4 63 same as ca-cp-nb + cp-cq-cq 62.640 124.470 SOURCE4 5 1.0864 + cq-cq-cq 72.200 90.000 SOURCE3 4 0.0000 +-cq-cq-nb 0.000 116.430 SOURCE3 2 0.0000 ++cq-cq-nb 68.050 116.600 SOURCE4 88 same as cp-cp-nb + s4-c -s4 98.110 108.810 SOURCE3 1=09 + s6-c -s6 95.130 115.750 SOURCE3 1=09 + sh-c -sh 100.060 115.330 SOURCE3 1 0.0000 +@@ -2454,9 +2426,6 @@ + n -cy-s6 82.570 103.450 SOURCE4 6 0.7197 + n -cy-ss 82.030 105.120 SOURCE4 69 0.3987 + nh-cz-nh 72.970 120.170 SOURCE4 26 0.3964 +-ca-i -cl 0.000 90.210 SOURCE3 2 estimated_force_cons= tant +-ca-i -o 0.000 97.080 SOURCE3 5 0.2233,estimated_for= ce_constant +-cl-i -cl 0.000 179.580 SOURCE3 1 estimated_force_cons= tant + br-n1-c1 51.100 180.000 HF/6-31G* 1=09 + c1-n1-c1 64.910 179.920 HF/6-31G* 1=09 + c1-n1-c2 60.250 177.730 HF/6-31G* 1=09 +@@ -2729,7 +2698,6 @@ + c2-n3-c2 66.220 124.680 SOURCE3 1=09 + c2-n3-hn 49.110 119.380 SOURCE3 1=09 + c3-n3-c3 64.010 110.900 SOURCE3 40 2.3048 +-c3-n3-ca 0.000 116.390 SOURCE3 1=09 + c3-n3-cl 62.170 107.230 SOURCE3 3 0.3673 + c3-n3-cx 62.450 116.320 SOURCE4 24 0.5119 + c3-n3-cy 61.690 118.260 SOURCE4 14 0.8788 +@@ -2753,7 +2721,6 @@ + c3-n3-sh 78.550 112.700 SOURCE3 1 0.0000 + c3-n3-ss 77.950 116.010 SOURCE3 3 1.1944 + c3-n3-sy 79.010 115.270 SOURCE4 108 1.7647 +-c -n3-c 0.000 127.170 SOURCE3 1=09 + cl-n3-cl 61.850 108.280 SOURCE3 1 0.0000 + cl-n3-hn 42.590 104.390 SOURCE3 2 0.0000 + cl-n3-n3 63.750 107.650 SOURCE3 1 0.0000 +@@ -2824,7 +2791,6 @@ + c1-n4-hn 48.620 110.190 SOURCE3 7 1.0847 + c2-n4-c2 63.010 112.580 SOURCE3 1 0.0000 + c2-n4-c3 63.100 110.960 SOURCE4 13 2.4632 +-c2-n4-h4 0.000 112.460 SOURCE3 1=09 + c2-n4-hn 46.430 111.360 SOURCE3 13 1.2672 + c3-n4-c3 62.840 110.640 SOURCE3 13 1.3060 + c3-n4-ca 63.610 110.400 SOURCE4 46 1.4643 +@@ -3002,10 +2968,6 @@ + ca-na-s 75.010 125.640 SOURCE3 1=09 + ca-na-sh 76.630 125.440 SOURCE3 1=09 + ca-na-ss 74.880 129.910 SOURCE4 8 0.1449 +-c -na-c 0.000 126.400 SOURCE3 1=09 +-c -na-c2 0.000 125.090 SOURCE3 1=09 +-c -na-c3 0.000 117.600 SOURCE3 1=09 +-c -na-ca 0.000 125.200 SOURCE3 1=09 + cc-na-cc 68.940 109.900 SOURCE3 109 1.5547 + cc-na-cd 63.880 128.010 SOURCE3 1 0.0000 + cc-na-ce 63.050 126.610 SOURCE4 8 0.5158 +@@ -3058,7 +3020,6 @@ + cd-na-s 74.800 125.660 SOURCE3 8 0.1880 + cd-na-sh 76.830 123.960 SOURCE3 10 0.3424 + cd-na-ss 77.930 119.180 SOURCE3 36 5.0538 +-c -na-hn 0.000 118.000 SOURCE3 1=09 + cl-na-cl 56.330 122.800 SOURCE3 1=09 + cl-na-nc 59.890 119.360 SOURCE3 4 1.7128 + cl-na-nd 59.890 119.360 SOURCE3 4 same_as_cl-na-nc +@@ -3067,7 +3028,6 @@ + cl-na-pc 58.780 120.510 SOURCE3 3 2.1985 + cl-na-pd 58.780 120.510 SOURCE3 3 same_as_cl-na-pc + cl-na-ss 77.180 111.910 SOURCE3 1 0.0000 +-c -na-n 0.000 124.660 SOURCE3 1=09 + f -na-f 62.220 120.200 SOURCE3 1=09 + f -na-nc 66.640 118.050 SOURCE3 4 1.7931 + f -na-nd 66.640 118.050 SOURCE3 4 same_as_f-na-nc +@@ -3231,7 +3191,7 @@ + sy-na-sy 96.930 123.200 SOURCE3 1=09 + ca-nb-ca 68.590 115.860 SOURCE3 46 1.1645 + ca-nb-cp 68.010 118.040 SOURCE4 58 0.7819 +-ca-nb-cq 0.000 117.040 SOURCE3 2 0.0000 ++ca-nb-cq 68.010 118.040 SOURCE4 58 same as ca-nb-cp + ca-nb-nb 69.370 118.890 SOURCE3 10 0.6031 + cp-nb-nb 68.790 121.110 SOURCE4 12 0.4315 + nb-nb-nb 70.440 121.040 SOURCE3 1 0.0000 +@@ -3597,8 +3557,6 @@ + ca-nh-sh 78.190 121.410 SOURCE3 1 0.0000 + ca-nh-ss 78.160 121.500 SOURCE3 3 2.6255 + ca-nh-sy 76.750 125.260 SOURCE4 41 1.7517 +-c -nh-c 0.000 119.570 SOURCE3 1=09 +-c -nh-ca 0.000 123.570 SOURCE3 1=09 + cc-nh-cx 63.320 122.820 SOURCE4 42 1.1841 + cc-nh-hn 48.860 117.160 SOURCE3 11 2.6137 + cc-nh-n2 68.230 119.660 SOURCE4 5 1.3903 +@@ -3610,10 +3568,8 @@ + ce-nh-sy 80.450 112.970 SOURCE4 7 1.0636 + cf-nh-hn 48.620 115.620 SOURCE4 16 1.3549 + cf-nh-o 67.070 129.430 SOURCE3 1 same_as_ce-nh-o +-c -nh-hn 0.000 115.730 SOURCE3 1=09 + cl-nh-cl 62.930 106.600 SOURCE3 1=09 + cl-nh-hn 43.080 104.140 SOURCE3 1 0.0000 +-c -nh-n4 0.000 111.350 SOURCE3 1=09 + cx-nh-cx 86.530 62.020 SOURCE4 45 0.6189 + cx-nh-hn 45.790 118.890 SOURCE4 8 0.1391 + cz-nh-hn 48.790 121.240 SOURCE4 40 0.5682 +@@ -3783,7 +3739,6 @@ + ho-oh-sh 54.390 106.240 SOURCE3 2 0.0661 + ho-oh-ss 54.540 107.060 SOURCE3 4 0.9967 + ho-oh-sy 55.940 106.410 SOURCE4 33 0.3729 +-Si-oh-ho 52.570 115.710 SOURCE4 5 0.1738 + br-os-br 65.080 110.630 SOURCE3 1 0.0000 + c1-os-c1 66.990 115.020 SOURCE3 1 0.0000 + c1-os-c3 64.470 113.390 SOURCE3 1 0.0000 +@@ -3892,7 +3847,6 @@ + s4-os-s4 99.450 111.630 SOURCE3 1 0.0000 + s6-os-s6 103.740 119.070 SOURCE3 2 0.4318 + sh-os-sh 97.950 118.950 SOURCE3 1 0.0000 +-Si-os-c3 74.830 124.640 SOURCE4 9 0.2879 + s -os-s 91.270 118.080 SOURCE3 1 0.0000 + ss-os-ss 97.420 115.640 SOURCE3 1 0.0000 + br-p2-br 65.020 108.600 SOURCE3 1=09 +@@ -4615,7 +4569,6 @@ + f -s4-f 43.790 92.710 SOURCE2 3 0.1490 + f -s4-o 43.870 106.810 SOURCE2 2 0.0100 + f -s4-s 47.340 107.500 SOURCE2 1 0.0000 +-hn-s4-hs 0.000 86.990 SOURCE3 1=09 + hs-s4-hs 23.650 87.000 SOURCE3 2 0.0202 + hs-s4-n1 32.050 90.510 HF/6-31G* 1=09 + hs-s4-o 31.160 110.270 SOURCE3 5 0.1908 +@@ -4789,12 +4742,6 @@ + hs-sh-s6 33.980 93.830 SOURCE3 3 1.2561 + hs-sh-sh 33.890 99.070 SOURCE3 2 0.0000 + hs-sh-ss 33.730 99.170 SOURCE3 3 0.2457 +-c3-Si-c3 34.810 109.820 SOURCE4 88 0.5569 +-c3-Si-ca 34.800 110.090 SOURCE4 26 0.7331 +-c3-Si-oh 38.160 107.440 SOURCE4 8 1.5150 +-c3-Si-os 38.140 108.750 SOURCE4 38 0.7301 +-ha-Si-ha 19.530 108.770 SOURCE4 5 0.5372 +-os-Si-os 42.630 108.350 SOURCE4 15 1.7995 + br-ss-br 41.920 102.920 SOURCE3 1 0.0000 + br-ss-c3 39.460 99.030 SOURCE3 1 0.0000 + c1-ss-c1 41.480 98.300 SOURCE2 1 0.0000 +@@ -4813,7 +4760,6 @@ + c3-ss-cl 37.940 99.400 SOURCE2 1 0.0000 + c3-ss-cy 38.750 94.320 SOURCE4 62 0.3646 + c3-ss-f 39.670 97.490 SOURCE3 1 0.0000 +-c3-ss-ha 0.000 96.500 SOURCE2 1 0.0000 + c3-ss-i 35.060 100.000 SOURCE3 1 0.0000 + c3-ss-n1 41.250 98.440 HF/6-31G* 1=09 + c3-ss-n2 41.260 96.420 SOURCE3 5 1.3604 +@@ -5883,7 +5829,7 @@ + were replaced with those newly generated. Here are the numbers: +=20 + Bond length: 59 low quality parameters were replaced and 56 new paramet= ers +-were introduced. $j ++were introduced. +=20 + Bond angle: 437 low quality parameters were replaced and 618 new + parameters were introduced.