Dear Amber Community,
Is there a way for TLEaP to ignore (instead of abort) if duplicate bonds are specified in the input file?
It’s easy enough to delete by hand duplicate bond definitions, but I’m working on an automated workflow. In a nutshell, if I have two residues that are ligands to two different cofactors parameterized with MCPB, and these residues happen to be adjacent in the primary sequence, my program writes the C(=O)-N bond definitions connecting each residue to the rest of the protein, without realizing that the C(=O)-N linkage between the two residues only needs to be specified once.
Of course, the nicest solution would be to revise my program to be smarter, but I haven’t figured out how to do that yet. (I’d appreciate any programming suggestions off-list!)
Best,
Matthew
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Received on Thu Dec 28 2023 - 09:30:03 PST
