+------------------------------------------------------------------------------+ |____/\/\______/\/\__/\/\/\/\/\/\__/\/\____/\/\________________________________| |____/\/\/\__/\/\/\______/\/\______/\/\__/\/\________/\/\__________/\/\________| |____/\/\/\/\/\/\/\______/\/\______/\/\/\/\______/\/\/\/\/\/\__/\/\/\/\/\/\____| |____/\/\__/\__/\/\______/\/\______/\/\__/\/\________/\/\__________/\/\________| |____/\/\______/\/\______/\/\______/\/\____/\/\________________________________| +------------------------------------------------------------------------------+ | | | ____ ____ | | / \ / \ | | / \/ \ | | \ / | | \ / | | / \ | | / \ | | \ /\ / | | \____/ \____/ | | | | 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 3PL1_settings.bcl loadParam 3PL1_params.xml loadLib 3PL1_stdMol.xml readPdb 3PL1 3PL1_large.pdb atomType assignConnectivity respgen /3PL1/3PL1_large 3PL1 3PL1_large quit ### ### ### ### ### ### ### ### ### MTK++ ### ### Function: elementParser ### ### Message: Reading XML with TINYXML ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: elementParser ### ### Message: Reading /home/pbalderaa/Documents/Amber/amber14/dat/mtkpp/elements.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: readInputFile ### ### Message: Commands read: set AMBERHOME $AMBERHOME set NAME 3PL1 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/pbalderaa/Documents/Amber/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/pbalderaa/Documents/Amber/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/pbalderaa/Documents/Amber/amber14/dat/mtkpp/metals/metalParm.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadLib ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: stdLibParser ### ### Message: Reading /home/pbalderaa/Documents/Amber/amber14/dat/mtkpp/amino94.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadLib ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: stdLibParser ### ### Message: Reading /home/pbalderaa/Documents/Amber/amber14/dat/mtkpp/aminont94.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadLib ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: stdLibParser ### ### Message: Reading /home/pbalderaa/Documents/Amber/amber14/dat/mtkpp/aminoct94.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadLib ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: stdLibParser ### ### Message: Reading /home/pbalderaa/Documents/Amber/amber14/dat/mtkpp/fragLib/terminal.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadLib ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: stdLibParser ### ### Message: Reading /home/pbalderaa/Documents/Amber/amber14/dat/mtkpp/metals/metals.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadParam ### ### ### ### ### ### ### ### ### MTK++ ### ### Function: paramParser ### ### Message: Reading XML with TINYXML ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: paramParser ### ### Message: Reading 3PL1_params.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: loadLib ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: stdLibParser ### ### Message: Reading 3PL1_stdMol.xml ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: readPdb ### ### ### ### ### ### ### ### ### MTK++ Warning ### ### Function: pdbParser ### ### Message: Can't determine 1-letter code for AS1. Using 'X'. ### ### ### ### ### ### ### ### ### MTK++ Warning ### ### Function: pdbParser ### ### Message: Can't determine 1-letter code for PH1. Using 'X'. ### ### ### ### ### ### ### ### ### MTK++ Warning ### ### Function: pdbParser ### ### Message: Can't determine 1-letter code for HDA. Using 'X'. ### ### ### ### ### ### ### ### ### MTK++ Warning ### ### Function: pdbParser ### ### Message: Can't determine 1-letter code for HDA. Using 'X'. ### ### ### ### ### ### ### ### ### MTK++ Warning ### ### Function: pdbParser ### ### Message: Can't determine 1-letter code for HDA. Using 'X'. ### ### ### ### ### ### ### ### ### MTK++ Warning ### ### Function: pdbParser ### ### Message: Can't determine 1-letter code for FE1. Using 'X'. ### ### ### ### ### ### ### ### ### MTK++ Warning ### ### Function: pdbParser ### ### Message: Can't determine 1-letter code for WT1. Using 'X'. ### ### ### ### ### ### ### ### ### MTK++ Warning ### ### Function: pdbParser ### ### Message: Can't determine 1-letter code for WT1. Using 'X'. ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: atomType ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: atomTyper::perceiveHistidines ### ### Message: Perceiving Histidine Residue Types ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: atomTyper::perceiveCysteines ### ### Message: Perceiving Cysteines Residue Types ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: atomTyper::atomTypeByLib ### ### Message: Residue: 0 Assigned HDA (l) Residue: 0 Assigned HDA (l) Residue: 0 Assigned HDA (l) Residue: 0 Assigned AS1 (l) Residue: 0 Assigned FE1 (m) Residue: 0 Assigned WT1 (m) Residue: 0 Assigned WT1 (m) ### ### ### ### ### ### ### ### ### MTK++ Warning ### ### Function: atomTyper::atomTypeByLib ### ### Message: Unable to assign stdFrag: unknown residue |PH1| ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: atomTyper::atomTypeByLib ### ### Message: Residue: 1 Assigned ACE (s) Residue: 2 Assigned AS1 (l) Residue: 4 Assigned HDA (l) Residue: 5 Assigned NME (e) Residue: 6 Assigned ACE (s) Residue: 7 Assigned HDA (l) Residue: 8 Assigned NME (e) Residue: 9 Assigned ACE (s) Residue: 10 Assigned HDA (l) Residue: 11 Assigned NME (e) Residue: 12 Assigned FE1 (m) Residue: 13 Assigned WT1 (m) Residue: 14 Assigned WT1 (m) ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: assignConnectivity ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::run ### ### Message: Collection Begin ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignBonds ### ### Message: Molecule Begin # 0 HDA: 0 bonds were added. HDA: 0 bonds were added. HDA: 0 bonds were added. AS1: 0 bonds were added. FE1: 0 bonds were added. WT1: 0 bonds were added. WT1: 0 bonds were added. ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignBonds ### ### Message: Molecule Begin # 1 ACE: 5 bonds were added. AS1: 12 bonds were added. PH1: 22 bonds were added. HDA: 17 bonds were added. NME: 6 bonds were added. ACE: 5 bonds were added. HDA: 18 bonds were added. NME: 6 bonds were added. ACE: 5 bonds were added. HDA: 18 bonds were added. NME: 6 bonds were added. FE1: 0 bonds were added. WT1: 3 bonds were added. WT1: 3 bonds were added. ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignAngles ### ### Message: Molecule # 0 0 angles were added ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignAngles ### ### Message: Molecule # 1 210 angles were added ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignTorsions ### ### Message: Molecule # 0 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignTorsions ### ### Message: 0 torsions were added ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignTorsions ### ### Message: Molecule # 1 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignTorsions ### ### Message: 275 torsions were added ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignImpropers ### ### Message: Molecule # 0 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignImpropers ### ### Message: Molecule # 1 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdBonds ### ### Message: Collection Begin ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdBonds ### ### Message: Molecule # 0 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdBonds ### ### Message: Molecule # 1 Unable to assign parameters for bond : N - C Unable to assign parameters for bond : N - CA Unable to assign parameters for bond : N - H Unable to assign parameters for bond : CA - C Unable to assign parameters for bond : CA - CB Unable to assign parameters for bond : CA - HA Unable to assign parameters for bond : C - O Unable to assign parameters for bond : C - N Unable to assign parameters for bond : CB - CG Unable to assign parameters for bond : CB - HB2 Unable to assign parameters for bond : CB - HB3 Unable to assign parameters for bond : CG - CD1 Unable to assign parameters for bond : CG - CD2 Unable to assign parameters for bond : CD1- CE1 Unable to assign parameters for bond : CD1- HD1 Unable to assign parameters for bond : CD2- CE2 Unable to assign parameters for bond : CD2- HD2 Unable to assign parameters for bond : CE1- CZ Unable to assign parameters for bond : CE1- HE1 Unable to assign parameters for bond : CE2- CZ Unable to assign parameters for bond : CE2- HE2 Unable to assign parameters for bond : CZ - HZ Total Number of Missing Bond Parameters = 22 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdAngles ### ### Message: Collection Begin ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdAngles ### ### Message: Molecule # 0 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdAngles ### ### Message: Molecule # 1 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdAngles ### ### Message: Unable to assign parameters for angle: HB2- CB - HB3 Unable to assign parameters for angle: CZ - CE1- HE1 Unable to assign parameters for angle: CZ - CE2- HE2 Unable to assign parameters for angle: CD2- CE2- CZ Unable to assign parameters for angle: CD2- CE2- HE2 Unable to assign parameters for angle: CB - CA - HA Unable to assign parameters for angle: CB - CG - CD1 Unable to assign parameters for angle: CB - CG - CD2 Unable to assign parameters for angle: CA - N - H Unable to assign parameters for angle: CA - C - O Unable to assign parameters for angle: CA - C - N Unable to assign parameters for angle: CA - CB - CG Unable to assign parameters for angle: CA - CB - HB2 Unable to assign parameters for angle: CA - CB - HB3 Unable to assign parameters for angle: CA - C - N Unable to assign parameters for angle: CE1- CD1- HD1 Unable to assign parameters for angle: CE1- CZ - CE2 Unable to assign parameters for angle: CE1- CZ - HZ Unable to assign parameters for angle: CG - CB - HB2 Unable to assign parameters for angle: CG - CB - HB3 Unable to assign parameters for angle: CG - CD1- CE1 Unable to assign parameters for angle: CG - CD1- HD1 Unable to assign parameters for angle: CG - CD2- CE2 Unable to assign parameters for angle: CG - CD2- HD2 Unable to assign parameters for angle: C - CA - CB Unable to assign parameters for angle: C - CA - HA Unable to assign parameters for angle: C - N - CA Unable to assign parameters for angle: C - N - H Unable to assign parameters for angle: C - N - CA Unable to assign parameters for angle: C - N - H Unable to assign parameters for angle: CE2- CD2- HD2 Unable to assign parameters for angle: CE2- CZ - HZ Unable to assign parameters for angle: CD1- CG - CD2 Unable to assign parameters for angle: CD1- CE1- CZ Unable to assign parameters for angle: CD1- CE1- HE1 Unable to assign parameters for angle: O - C - N Unable to assign parameters for angle: N - CA - C Unable to assign parameters for angle: N - CA - CB Unable to assign parameters for angle: N - CA - HA Unable to assign parameters for angle: O - C - N Total Number of Missing Angle Parameters = 40 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdTorsions ### ### Message: Collection Begin ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdTorsions ### ### Message: Molecule # 0 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdTorsions ### ### Message: Molecule # 1 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: connections::assignStdTorsions ### ### Message: Unable to assign parameters for torsion: CG - CD2- CE2- CZ Unable to assign parameters for torsion: CG - CD2- CE2- HE2 Unable to assign parameters for torsion: CG - CB - CA - HA Unable to assign parameters for torsion: HE2- CE2- CD2- HD2 Unable to assign parameters for torsion: C - N - CA - C Unable to assign parameters for torsion: C - N - CA - CB Unable to assign parameters for torsion: C - N - CA - HA Unable to assign parameters for torsion: O - C - CA - CB Unable to assign parameters for torsion: O - C - CA - HA Unable to assign parameters for torsion: O - C - N - CA Unable to assign parameters for torsion: O - C - N - H Unable to assign parameters for torsion: C - CA - N - H Unable to assign parameters for torsion: C - CA - CB - CG Unable to assign parameters for torsion: C - CA - CB - HB2 Unable to assign parameters for torsion: C - CA - CB - HB3 Unable to assign parameters for torsion: HD1- CD1- CE1- HE1 Unable to assign parameters for torsion: CA - C - N - CA Unable to assign parameters for torsion: CA - C - N - H Unable to assign parameters for torsion: N - CA - C - N Unable to assign parameters for torsion: C - N - CA - C Unable to assign parameters for torsion: C - N - CA - CB Unable to assign parameters for torsion: C - N - CA - HA Unable to assign parameters for torsion: CB - CA - N - H Unable to assign parameters for torsion: CB - CA - C - N Unable to assign parameters for torsion: O - C - N - CA Unable to assign parameters for torsion: O - C - N - H Unable to assign parameters for torsion: HE1- CE1- CZ - HZ Unable to assign parameters for torsion: CA - CB - CG - CD1 Unable to assign parameters for torsion: CA - CB - CG - CD2 Unable to assign parameters for torsion: HA - CA - C - N Unable to assign parameters for torsion: HA - CA - CB - HB2 Unable to assign parameters for torsion: HA - CA - CB - HB3 Unable to assign parameters for torsion: CZ - CE1- CD1- HD1 Unable to assign parameters for torsion: CE2- CZ - CE1- HE1 Unable to assign parameters for torsion: H - N - CA - HA Unable to assign parameters for torsion: CD2- CG - CB - HB2 Unable to assign parameters for torsion: CD2- CG - CB - HB3 Unable to assign parameters for torsion: CD2- CG - CD1- CE1 Unable to assign parameters for torsion: CD2- CG - CD1- HD1 Unable to assign parameters for torsion: CG - CD1- CE1- CZ Unable to assign parameters for torsion: CG - CD1- CE1- HE1 Unable to assign parameters for torsion: CB - CG - CD1- CE1 Unable to assign parameters for torsion: CB - CG - CD1- HD1 Unable to assign parameters for torsion: CB - CG - CD2- CE2 Unable to assign parameters for torsion: CB - CG - CD2- HD2 Unable to assign parameters for torsion: HZ - CZ - CE2- HE2 Unable to assign parameters for torsion: CB - CA - C - N Unable to assign parameters for torsion: CA - C - N - CA Unable to assign parameters for torsion: CA - C - N - H Unable to assign parameters for torsion: N - CA - C - O Unable to assign parameters for torsion: N - CA - C - N Unable to assign parameters for torsion: N - CA - CB - CG Unable to assign parameters for torsion: N - CA - CB - HB2 Unable to assign parameters for torsion: N - CA - CB - HB3 Unable to assign parameters for torsion: CZ - CE2- CD2- HD2 Unable to assign parameters for torsion: CE1- CZ - CE2- HE2 Unable to assign parameters for torsion: HA - CA - C - N Unable to assign parameters for torsion: CD2- CE2- CZ - CE1 Unable to assign parameters for torsion: CD2- CE2- CZ - HZ Unable to assign parameters for torsion: CD1- CE1- CZ - CE2 Unable to assign parameters for torsion: CD1- CE1- CZ - HZ Unable to assign parameters for torsion: CD1- CG - CB - HB2 Unable to assign parameters for torsion: CD1- CG - CB - HB3 Unable to assign parameters for torsion: CD1- CG - CD2- CE2 Unable to assign parameters for torsion: CD1- CG - CD2- HD2 Total Number of Missing Torsion Parameters = 65 ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: MCPB ### ### Message: respgen ### ### ### ### ### ### ### ### ### MTK++ Info ### ### Function: selection::parse ### ### Message: selection string = /3PL1/3PL1_large ### ### ### ###