Dear AMBER community,
The “small model” built by MCPB for my system undergoes a rearrangement upon optimization that is not consistent with the crystal structure and does not happen if I fully optimize the "large model” built by MCPB.
Is it possible to have the small model be the same as the large model for parameterization by MCPB? Or, to enlarge the small model to include the extra groups found in the large model?
I’ve tried additional_resids, but this keyword only seems to add the side chains of the additional residues. In an optimization, those side chains will just fly away. Is there a way to include the backbone of the additional residues? (By additional, I’m thinking of including the preceding and proceeding residue to the one that is coordinated.)
Best,
Matthew
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Received on Sun Oct 23 2022 - 15:30:03 PDT
