source 1AMP_OH_settings.bcl # Load AMBER Parameters loadParam NAME_params_fc_md.xml # Load AMBER libraries # loadLib NAME_chg2.xml loadLib NAME_stdMol.xml # Read pdb readPdb NAME NAME_fixed_H.pdb # Assign S-S bonds assignDisulfideBonds # Atom type atomType # Assign bonds, angles, and torsions assignConnectivity # Find metal centers findMetalCenters # print / # Write leaprc file writeLeap NAME NAME_mcpb.pdb # Write pdb with new residue names writePdb NAME_mcpb.pdb # Exit MCPB quit