# Load settings source lac_3CU_settings.bcl # Create non-standard residue library createStdGroup NAME copyStdResidue aminoAcids94/HID NAME/HD0 copyStdResidue aminoAcids94/HIE NAME/HE1 copyStdResidue aminoAcids94/HID NAME/HD2 copyStdResidue aminoAcids94/HID NAME/HD3 #copyStdResidue aminoAcids94/HIE NAME/HE4 copyStdResidue aminoAcids94/HID NAME/HD5 copyStdResidue aminoAcids94/HID NAME/HD6 copyStdResidue aminoAcids94/HID NAME/HD7 copyStdResidue aminoAcids94/HID NAME/HD8 #copyStdResidue aminoAcids94/HIE NAME/HE9 #copyStdResidue aminoAcids94/CYM NAME/CM1 copyStdResidue aminoAcids94/MOH NAME/MH1 copyStdResidue aminoAcids94/MOH NAME/MH2 #copyStdResidue metals/.CU NAME/CU1 copyStdResidue metals/.CU NAME/CU2 copyStdResidue metals/.CU NAME/CU3 copyStdResidue metals/.CU NAME/CU4 # write standard library writeLib NAME NAME.xml # Open PDB file readPdb NAME NAME_fixed_H.pdb # Assign S-S bonds assignDisulfideBonds # Atom type atomType # Assign bonds, angles, and torsions assignConnectivity # Add hydrogens #addHs /NAME/ #################### CLUSTER #################### # Create molecule named CLR createMolecule CLR # Create HE4-1 from HIE-395 #createResidue HE4 in CLR #addToResidue /NAME/CLR/HE4 /NAME/1/HIE-395 not bb # Create HE9-2 from HIE-458 #createResidue HE9 in CLR #addToResidue /NAME/CLR/HE9 /NAME/1/HIE-458 not bb # Create CM1-3 from CYM-453 #createResidue CM1 in CLR #addToResidue /NAME/CLR/CM1 /NAME/1/CYM-453 not bb # Create HD0-4 from HID-64 createResidue HD0 in CLR addToResidue /NAME/CLR/HD0 /NAME/1/HID-64 not bb # Create HD5-5 from HID-398 createResidue HD5 in CLR addToResidue /NAME/CLR/HD5 /NAME/1/HID-398 not bb # Create HE1-6 from HIE-66 createResidue HE1 in CLR addToResidue /NAME/CLR/HE1 /NAME/1/HIE-66 not bb # Create HD2-7 from HID-109 createResidue HD2 in CLR addToResidue /NAME/CLR/HD2 /NAME/1/HID-109 not bb # Create HD8-8 from HID-454 createResidue HD8 in CLR addToResidue /NAME/CLR/HD8 /NAME/1/HID-454 not bb # Create HD3-9 from HID-111 createResidue HD3 in CLR addToResidue /NAME/CLR/HD3 /NAME/1/HID-111 not bb # Create HD6-10 from HID-400 createResidue HD6 in CLR addToResidue /NAME/CLR/HD6 /NAME/1/HID-400 not bb # Create HD7-11 from HID-452 createResidue HD7 in CLR addToResidue /NAME/CLR/HD7 /NAME/1/HID-452 not bb # Create CU1-12 from CU-500 #createResidue CU1 in CLR #addToResidue /NAME/CLR/CU1 /NAME/2/.CU-500/CU.. # Create CU2-13 from CU-503 createResidue CU2 in CLR addToResidue /NAME/CLR/CU2 /NAME/3/.CU-501/CU.. # Create CU3-14 from CU-501 createResidue CU3 in CLR addToResidue /NAME/CLR/CU3 /NAME/4/.CU-502/CU.. # Create CU4-15 from CU-502 createResidue CU4 in CLR addToResidue /NAME/CLR/CU4 /NAME/5/.CU-503/CU.. # Create MH1-16 from MOH-1505 createResidue MH1 in CLR addToResidue /NAME/CLR/MH1 /NAME//MOH-1505 # Create MH2-17 from MOH-1540 createResidue MH2 in CLR addToResidue /NAME/CLR/MH2 /NAME//MOH-1540 # Add methyl group to the residue sidechains(use the methyl group to replace # the CA atom of each sidechain). Here we define the methyl group has bond, # angle and torsion with the other three sidechain atoms. The dihedral values # is the dihedral value of the four atoms (CA atom with the other three atoms) # are from PDB structure, which may be different for different residues in # different PDB file. You need to check the PDB file manually by yourself. #addFragment terminal/CH3 bd /NAME/CLR/HE4-1/.CB. ag /NAME/CLR/HE4-1/.CG. tr /NAME/CLR/HE4-1/.ND1 287.0 #addFragment terminal/CH3 bd /NAME/CLR/HE9-2/.CB. ag /NAME/CLR/HE9-2/.CG. tr /NAME/CLR/HE9-2/.ND1 82.0 #addFragment terminal/CH3 bd /NAME/CLR/CM1-3/.CB. ag /NAME/CLR/CM1-3/.CG. tr /NAME/CLR/CU1-4/CU.. 178.8 addFragment terminal/CH3 bd /NAME/CLR/HD0-4/.CB. ag /NAME/CLR/HD0-4/.CG. tr /NAME/CLR/HD0-4/.ND1 64.0 addFragment terminal/CH3 bd /NAME/CLR/HD5-5/.CB. ag /NAME/CLR/HD5-5/.CG. tr /NAME/CLR/HD5-5/.ND1 51.0 addFragment terminal/CH3 bd /NAME/CLR/HE1-6/.CB. ag /NAME/CLR/HE1-6/.CG. tr /NAME/CLR/HE1-6/.ND1 124.0 addFragment terminal/CH3 bd /NAME/CLR/HD2-7/.CB. ag /NAME/CLR/HD2-7/.CG. tr /NAME/CLR/HD2-7/.ND1 83.0 addFragment terminal/CH3 bd /NAME/CLR/HD8-8/.CB. ag /NAME/CLR/HD8-8/.CG. tr /NAME/CLR/HD8-8/.ND1 298.0 addFragment terminal/CH3 bd /NAME/CLR/HD3-9/.CB. ag /NAME/CLR/HD3-9/.CG. tr /NAME/CLR/HD3-9/.ND1 300.0 addFragment terminal/CH3 bd /NAME/CLR/HD6-10/.CB. ag /NAME/CLR/HD6-10/.CG. tr /NAME/CLR/HD6-10/.ND1 245.0 addFragment terminal/CH3 bd /NAME/CLR/HD7-11/.CB. ag /NAME/CLR/HD7-11/.CG. tr /NAME/CLR/HD7-11/.ND1 80.0 # Create bonds with copper1 #createBond /NAME/CLR/CU1/CU.. /NAME/CLR/HE4/.NE2 #createBond /NAME/CLR/CU1/CU.. /NAME/CLR/HE9/.NE2 #createBond /NAME/CLR/CU1/CU.. /NAME/CLR/CM1/.SG # Create bonds with copper2 createBond /NAME/CLR/CU2/CU.. /NAME/CLR/HD0/.NE2 createBond /NAME/CLR/CU2/CU.. /NAME/CLR/HD5/.NE2 createBond /NAME/CLR/CU2/CU.. /NAME/CLR/MH2/.O.. # Create bonds with copper3 createBond /NAME/CLR/CU3/CU.. /NAME/CLR/HE1/.NE2 createBond /NAME/CLR/CU3/CU.. /NAME/CLR/HD2/.NE2 createBond /NAME/CLR/CU3/CU.. /NAME/CLR/HD8/.NE2 createBond /NAME/CLR/CU3/CU.. /NAME/CLR/MH1/.O.. # Create bonds with copper4 createBond /NAME/CLR/CU4/CU.. /NAME/CLR/HD3/.NE2 createBond /NAME/CLR/CU4/CU.. /NAME/CLR/HD6/.NE2 createBond /NAME/CLR/CU4/CU.. /NAME/CLR/HD7/.NE2 createBond /NAME/CLR/CU4/CU.. /NAME/CLR/MH1/.O.. # Atomtype atomType /NAME/CLR # Assign bonds and angles assignParameters /NAME/CLR # Add Bond and Angle Parameters addBondAndAngleParameters /NAME/CLR NAME # Write FRCMOD file writeParams NAME NAME_params.xml # Write pdb/mol files writePdb /NAME/CLR NAME_sidechain.pdb writeMol /NAME/CLR NAME_sidechain.mol writeSdf /NAME/CLR NAME_sidechain.sdf # Gaussian options levelOfTheory B3LYP basisSet 6-31G* clusterCharge CLR 12 clusterSpin 4 gaussianNProc 2 gaussianMem 3000MB # Set Gaussian input name --> Optimize and get force constants gaussianOptAndFC /NAME/CLR NAME_sidechain.com # Exit MCPB quit