+------------------------------------------------------------------------------+
|____/\/\______/\/\__/\/\/\/\/\/\__/\/\____/\/\________________________________|
|____/\/\/\__/\/\/\______/\/\______/\/\__/\/\________/\/\__________/\/\________|
|____/\/\/\/\/\/\/\______/\/\______/\/\/\/\______/\/\/\/\/\/\__/\/\/\/\/\/\____|
|____/\/\__/\__/\/\______/\/\______/\/\__/\/\________/\/\__________/\/\________|
|____/\/\______/\/\______/\/\______/\/\____/\/\________________________________|
+------------------------------------------------------------------------------+
|                                                                              |
|                                 ____    ____                                 |
|                                /    \  /    \                                |
|                               /      \/      \                               |
|                               \              /                               |
|                                \            /                                |
|                                /            \                                |
|                               /              \                               |
|                               \      /\      /                               |
|                                \____/  \____/                                |
|                                                                              |
|                                 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 <http://www.gnu.org/licenses/>.        |
|                                                                              |
+------------------------------------------------------------------------------+
|                                                                              |
| 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/ASP NAME/AS1
copyStdResidue aminoAcids94/HID NAME/HD1
copyStdResidue aminoAcids94/GLU NAME/GL1
copyStdResidue aminoAcids94/HID NAME/HD2
copyStdResidue aminoAcids94/ASP NAME/AS2
copyStdResidue aminoAcids94/MOH NAME/OH1
copyStdResidue metals/.ZN NAME/ZN1
copyStdResidue metals/.ZN NAME/ZN2
copyAtomType parm94/O2 NAME/OA
copyAtomType parm94/O2 NAME/OB
copyAtomType parm94/O2 NAME/OC
setAtomType NAME/AS1/.OD1 NAME/OA
setAtomType NAME/AS1/.OD2 NAME/OA
setAtomType NAME/GL1/.OE1 NAME/OB
setAtomType NAME/GL1/.OE2 NAME/OB
setAtomType NAME/AS2/.OD1 NAME/OC
setAtomType NAME/AS2/.OD2 NAME/OC
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-97 not bb
createResidue AS2 in CLR
addToResidue /NAME/CLR/AS2 /NAME/1/ASP-179 not bb
createResidue AS1 in CLR
addToResidue /NAME/CLR/AS1 /NAME/1/ASP-117 not bb
createResidue GL1 in CLR
addToResidue /NAME/CLR/GL1 /NAME/1/GLU-152 not bb
createResidue HD2 in CLR
addToResidue /NAME/CLR/HD2 /NAME/1/HID-256 not bb
createResidue ZN1 in CLR
addToResidue /NAME/CLR/ZN1 /NAME/2/.ZN-501/ZN..
createResidue ZN2 in CLR
addToResidue /NAME/CLR/ZN2 /NAME/3/.ZN-502/ZN..
createResidue OH1 in CLR
addToResidue /NAME/CLR/OH1 /NAME//MOH-935
addFragment terminal/CH3 bd /NAME/CLR/HD1-1/.CB. ag /NAME/CLR/HD1-1/.CG. tr /NAME/CLR/HD1-1/.ND1 87.0
addFragment terminal/CH3 bd /NAME/CLR/AS2-2/.CB. ag /NAME/CLR/AS2-2/.CG. tr /NAME/CLR/AS2-2/.OD2 170.0
addFragment terminal/CH3 bd /NAME/CLR/AS1-3/.CB. ag /NAME/CLR/AS1-3/.CG. tr /NAME/CLR/AS1-3/.OD2 200.0
addFragment terminal/CH3 bd /NAME/CLR/GL1-4/.CB. ag /NAME/CLR/GL1-4/.CG. tr /NAME/CLR/GL1-4/.CD. 288.0
addFragment terminal/CH3 bd /NAME/CLR/HD2-5/.CB. ag /NAME/CLR/HD2-5/.CG. tr /NAME/CLR/HD2-5/.ND1 185.0
createBond /NAME/CLR/ZN1/ZN.. /NAME/CLR/HD2/.NE2
createBond /NAME/CLR/ZN1/ZN.. /NAME/CLR/AS1/.OD2
createBond /NAME/CLR/ZN1/ZN.. /NAME/CLR/GL1/.OE2
createBond /NAME/CLR/ZN1/ZN.. /NAME/CLR/OH1/.O..
createBond /NAME/CLR/ZN2/ZN.. /NAME/CLR/HD1/.NE2
createBond /NAME/CLR/ZN2/ZN.. /NAME/CLR/AS1/.OD1
createBond /NAME/CLR/ZN2/ZN.. /NAME/CLR/AS2/.OD1
createBond /NAME/CLR/ZN2/ZN.. /NAME/CLR/OH1/.O..
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 0
clusterSpin 1
g03nProc 2
g03Mem 3000MB
g03OptAndFC /NAME/CLR NAME_sidechain.com
quit

 ### ### ### ###