Re: [AMBER] MMPBSA problem

From: David A Case via AMBER <>
Date: Tue, 28 Feb 2023 08:42:28 -0500

On Fri, Feb 24, 2023, Jurica Novak via AMBER wrote:
>For some reason, the files generated by do not have the
>correct number of atoms - _MMPBSA_complex.pdb, _MMPBSA_receptor.pdb, and
>_MMPBSA_ligand.pdb are the same files, all containing only the receptor.

Something must be going wrong at the preparation stage: did you use This script tries to guess what the ligand and receptor
are, but is not foolproof. You may need to generate the prmtop/inpcrd files
by hand. Or at least, provide info about how you carried out the
preparation steps, in case some operator error is involved. Is there
anything different about the systems that worked OK and those that failed,
especially in regards to how clear it is what is the receptor and what is
the ligand?


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Received on Tue Feb 28 2023 - 06:00:03 PST
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