diff --git a/src/tools/MolDataClass.cpp b/src/tools/MolDataClass.cpp index c29f1382045859f8415092170f0aa3cd9a58bc35..c6c43092d9c91d784e1d71a82f74949b4d545071 100644 --- a/src/tools/MolDataClass.cpp +++ b/src/tools/MolDataClass.cpp @@ -134,6 +134,25 @@ void MolDataClass::specialSymbol( const std::string& type, const std::string& sy numbers[1]=mypdb.getNamedAtomFromResidue("C",resnum); numbers[2]=mypdb.getNamedAtomFromResidue("N",resnum+1); numbers[3]=mypdb.getNamedAtomFromResidue("CA",resnum+1); + } else if( symbol.find("chi1")!=std::string::npos ){ + std::size_t dash=symbol.find_first_of('-'); + unsigned resnum; Tools::convert( symbol.substr(dash+1), resnum ); + std::string resname = mypdb.getResidueName(resnum); + if( !allowedResidue( type, resname ) || isTerminalGroup( type, resname ) ) return ; + if ( resname=="GLY" || resname=="ALA" ) plumed_merror("chi-1 is not defined for Alanine and Glycine"); + numbers.resize(4); + numbers[0]=mypdb.getNamedAtomFromResidue("N",resnum); + numbers[1]=mypdb.getNamedAtomFromResidue("CA",resnum); + numbers[2]=mypdb.getNamedAtomFromResidue("CB",resnum); + if(resname=="ILE"||resname=="VAL") + numbers[3]=mypdb.getNamedAtomFromResidue("CG1",resnum); + else if(resname=="CYS") + numbers[3]=mypdb.getNamedAtomFromResidue("SG",resnum); + else if(resname=="THR") + numbers[3]=mypdb.getNamedAtomFromResidue("OG1",resnum); + else if(resname=="SER") + numbers[3]=mypdb.getNamedAtomFromResidue("OG",resnum); + else numbers[3]=mypdb.getNamedAtomFromResidue("CG",resnum); } } else { plumed_merror(type + " is not a valid molecule type");