+------------------------------------------------------------------------------+ |____/\/\______/\/\__/\/\/\/\/\/\__/\/\____/\/\________________________________| |____/\/\/\__/\/\/\______/\/\______/\/\__/\/\________/\/\__________/\/\________| |____/\/\/\/\/\/\/\______/\/\______/\/\/\/\______/\/\/\/\/\/\__/\/\/\/\/\/\____| |____/\/\__/\__/\/\______/\/\______/\/\__/\/\________/\/\__________/\/\________| |____/\/\______/\/\______/\/\______/\/\____/\/\________________________________| +------------------------------------------------------------------------------+ | | | ____ ____ | | / \ / \ | | / \/ \ | | \ / | | \ / | | / \ | | / \ | | \ /\ / | | \____/ \____/ | | | | MTK++ 0.2.0 | | | | Copyright (C) 2005-2010 (see AUTHORS file for a list of contributors) | | | | MTK++ is free software; you can redistribute it and/or modify | | it under the terms of the GNU Lesser General Public License as published by | | the Free Software Foundation; either version 3 of the License, or | | (at your option) any later version. | | | | MTK++ is distributed in the hope that it will be useful, | | but WITHOUT ANY WARRANTY; without even the implied warranty of | | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | | GNU Lessser General Public License for more details. | | | | You should have received a copy of the GNU Lesser General Public License | | along with this program. If not, see . | | | +------------------------------------------------------------------------------+ | | | This program uses the MTK++ package. | | | +------------------------------------------------------------------------------+ | | | MCPB | | Martin B. Peters | | Copyright (c) 2005-2011 | | All Rights Reserved. | | | +------------------------------------------------------------------------------+ ### ### ### ### ### MTK++ Info ### ### Function: readInputFile ### ### Message: Commands read: source 1AMP_OH_settings.bcl createStdGroup NAME copyStdResidue aminoAcids94/HID NAME/HD1 copyStdResidue aminoAcids94/GLU NAME/GL1 copyStdResidue aminoAcids94/HID NAME/HD2 copyStdResidue aminoAcids94/MOH NAME/OH1 copyStdResidue aminoAcids94/SOH NAME/SH1 copyStdResidue metals/.FE NAME/FE1 copyAtomType parm94/O2 NAME/OB setAtomType NAME/GL1/.OE1 NAME/OB setAtomType NAME/GL1/.OE2 NAME/OB writeLib NAME NAME.xml readPdb NAME NAME_fixed.pdb assignDisulfideBonds atomType assignConnectivity addHs /NAME/ createMolecule CLR createResidue HD1 in CLR addToResidue /NAME/CLR/HD1 /NAME/1/HID-132 not bb createResidue GL1 in CLR addToResidue /NAME/CLR/GL1 /NAME/1/GLU-136 not bb createResidue HD2 in CLR addToResidue /NAME/CLR/HD2 /NAME/1/HID-174 not bb createResidue ZN1 in CLR addToResidue /NAME/CLR/FE1 /NAME/2/FE2-386/FE.. createResidue OH1 in CLR addToResidue /NAME/CLR/OH1 /NAME//MOH-425 createResidue SH1 in CLR addToResidue /NAME/CLR/SH1 /NAME//MOH-387 addFragment terminal/CH3 bd /NAME/CLR/HD1-1/.CB. ag /NAME/CLR/HD1-1/.CG. tr /NAME/CLR/HD1-1/.ND1 55.5 addFragment terminal/CH3 bd /NAME/CLR/GL1-2/.CB. ag /NAME/CLR/GL1-2/.CG. tr /NAME/CLR/GL1-2/.CD. -178.8 addFragment terminal/CH3 bd /NAME/CLR/HD2-5/.CB. ag /NAME/CLR/HD2-5/.CG. tr /NAME/CLR/HD2-5/.CD2 99.2 createBond /NAME/CLR/FE1/FE.. /NAME/CLR/HD1/.NE2 createBond /NAME/CLR/FE1/FE.. /NAME/CLR/HD2/.NE2 createBond /NAME/CLR/FE1/FE.. /NAME/CLR/GL1/.OE2 createBond /NAME/CLR/FE1/FE.. /NAME/CLR/OH1/.O.. createBond /NAME/CLR/FE1/FE.. /NAME/CLR/SH1/.O14 atomType /NAME/CLR assignParameters /NAME/CLR addBondAndAngleParameters /NAME/CLR NAME writeParams NAME NAME_params.xml writePdb /NAME/CLR NAME_sidechain.pdb writeMol /NAME/CLR NAME_sidechain.mol writeSdf /NAME/CLR NAME_sidechain.sdf levelOfTheory B3LYP basisSet 6-31G* clusterCharge CLR -1 clusterSpin 5 gaussianNProc 16 gaussianMem 6000MB gaussianOptAndFC /NAME/CLR NAME_sidechain.com quit ### ### ### ### ### ### ### ### ### MTK++ ### ### Function: elementParser ### ### Message: Reading XML with TINYXML ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: elementParser ### ### Message: Reading /home/kddubey/softwares/amber14//dat/mtkpp/elements.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: readInputFile ### ### Message: Commands read: set AMBERHOME $AMBERHOME set NAME 1AMP_OH loadParam AMBERHOME/dat/mtkpp/parm94.xml loadParam AMBERHOME/dat/mtkpp/parm_gaff.xml loadParam AMBERHOME/dat/mtkpp/metals/metalParm.xml loadLib AMBERHOME/dat/mtkpp/amino94.xml loadLib AMBERHOME/dat/mtkpp/aminont94.xml loadLib AMBERHOME/dat/mtkpp/aminoct94.xml loadLib AMBERHOME/dat/mtkpp/fragLib/terminal.xml loadLib AMBERHOME/dat/mtkpp/metals/metals.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: set ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: set ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadParam ### ### ### ### ### ### ### ### ### MTK++ ### ### Function: paramParser ### ### Message: Reading XML with TINYXML ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: paramParser ### ### Message: Reading /home/kddubey/softwares/amber14//dat/mtkpp/parm94.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadParam ### ### ### ### ### ### ### ### ### MTK++ ### ### Function: paramParser ### ### Message: Reading XML with TINYXML ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: paramParser ### ### Message: Reading /home/kddubey/softwares/amber14//dat/mtkpp/parm_gaff.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadParam ### ### ### ### ### ### ### ### ### MTK++ ### ### Function: paramParser ### ### Message: Reading XML with TINYXML ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: paramParser ### ### Message: Reading /home/kddubey/softwares/amber14//dat/mtkpp/metals/metalParm.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadLib ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: stdLibParser ### ### Message: Reading /home/kddubey/softwares/amber14//dat/mtkpp/amino94.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadLib ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: stdLibParser ### ### Message: Reading /home/kddubey/softwares/amber14//dat/mtkpp/aminont94.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadLib ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: stdLibParser ### ### Message: Reading /home/kddubey/softwares/amber14//dat/mtkpp/aminoct94.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadLib ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: stdLibParser ### ### Message: Reading /home/kddubey/softwares/amber14//dat/mtkpp/fragLib/terminal.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadLib ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: stdLibParser ### ### Message: Reading /home/kddubey/softwares/amber14//dat/mtkpp/metals/metals.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: createStdGroup ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: copyStdResidue ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: copyStdResidue ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: copyStdResidue ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: copyStdResidue ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: copyStdResidue ### ### ### ### ### ### ### ### ### MTK++ Error ### ### Function: MCPB::copyStdResidue ### ### Message: Incorrect use of copyStdResidue ### ### ### ###