# Load settings source TYRO_OH_settings.bcl # Create non-standard residue library createStdGroup NAME copyStdResidue aminoAcids94/HID NAME/HD1 copyStdResidue aminoAcids94/HID NAME/HD2 copyStdResidue aminoAcids94/HID NAME/HD3 copyStdResidue aminoAcids94/HID NAME/HD4 copyStdResidue aminoAcids94/HID NAME/HD5 copyStdResidue aminoAcids94/HID NAME/HD6 copyStdResidue aminoAcids94/MOH NAME/OH1 copyStdResidue metals/.ZN NAME/ZN1 copyStdResidue metals/.ZN NAME/ZN2 # write standard library writeLib NAME NAME.xml # Open PDB file readPdb NAME NAME_fixed.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 HD1-1 from HID-65 createResidue HD1 in CLR addToResidue /NAME/CLR/HD1 /NAME/1/HID-65 not bb # Create HD2-2 from HID-87 createResidue HD2 in CLR addToResidue /NAME/CLR/HD2 /NAME/1/HID-87 not bb # Create HD3-3 from HID-96 createResidue HD3 in CLR addToResidue /NAME/CLR/HD3 /NAME/1/HID-96 not bb # Create HD4-4 from HID-248 createResidue HD4 in CLR addToResidue /NAME/CLR/HD4 /NAME/1/HID-248 not bb # Create HD5-5 from HID-252 createResidue HD5 in CLR addToResidue /NAME/CLR/HD5 /NAME/1/HID-252 not bb # Create HD6-6 from HID-275 createResidue HD6 in CLR addToResidue /NAME/CLR/HD6 /NAME/1/HID-275 not bb # Create ZN1-7 from ZN-337 createResidue ZN1 in CLR addToResidue /NAME/CLR/ZN1 /NAME/2/.ZN-337/ZN.. # Create ZN2-8 from ZN-338 createResidue ZN2 in CLR addToResidue /NAME/CLR/ZN2 /NAME/3/.ZN-338/ZN.. # Create OH1-9 from HOH-378 createResidue OH1 in CLR addToResidue /NAME/CLR/OH1 /NAME//MOH-378 # 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/HD1-1/.CB. ag /NAME/CLR/HD1-1/.CG. tr /NAME/CLR/HD1-1/.ND1 278.8 addFragment terminal/CH3 bd /NAME/CLR/HD2-2/.CB. ag /NAME/CLR/HD2-2/.CG. tr /NAME/CLR/HD2-2/.ND1 70.6 addFragment terminal/CH3 bd /NAME/CLR/HD3-3/.CB. ag /NAME/CLR/HD3-3/.CG. tr /NAME/CLR/HD3-3/.ND1 97.4 addFragment terminal/CH3 bd /NAME/CLR/HD4-4/.CB. ag /NAME/CLR/HD4-4/.CG. tr /NAME/CLR/HD4-4/.ND1 276.9 addFragment terminal/CH3 bd /NAME/CLR/HD5-5/.CB. ag /NAME/CLR/HD5-5/.CG. tr /NAME/CLR/HD5-5/.ND1 287.9 addFragment terminal/CH3 bd /NAME/CLR/HD6-6/.CB. ag /NAME/CLR/HD6-6/.CG. tr /NAME/CLR/HD6-6/.ND1 271.3 # Create bonds with cooper1 createBond /NAME/CLR/ZN1/ZN.. /NAME/CLR/HD1/.NE2 createBond /NAME/CLR/ZN1/ZN.. /NAME/CLR/HD2/.NE2 createBond /NAME/CLR/ZN1/ZN.. /NAME/CLR/HD3/.NE2 createBond /NAME/CLR/ZN1/ZN.. /NAME/CLR/OH1/.O.. # Create bonds with cooper2 createBond /NAME/CLR/ZN2/ZN.. /NAME/CLR/HD4/.NE2 createBond /NAME/CLR/ZN2/ZN.. /NAME/CLR/HD5/.NE2 createBond /NAME/CLR/ZN2/ZN.. /NAME/CLR/HD6/.NE2 createBond /NAME/CLR/ZN2/ZN.. /NAME/CLR/OH1/.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 0 clusterSpin 1 gaussianNProc 12 gaussianMem 20GB # Set Gaussian input name --> Optimize and get force constants gaussianOptAndFC /NAME/CLR NAME_sidechain.com # Exit MCPB quit