Re: [AMBER] Parmed: Residues cannot be part of 2 molecules! Molecule section will not be correctly set.

From: David A Case <>
Date: Thu, 6 Aug 2020 16:30:16 -0400

On Thu, Aug 06, 2020, Samuel A. Ratliff wrote:
>I've found an issue in my .prmtop file that is caused by creating a bond
>in tleap between a protein and its heme.

Modify the pdb file so that the heme group directly follows the protein chain
to which it will be attached.

[Amber developers: does anyone know which parts of the code still need to know
where the "molecules" are? I suspect we only have a molecular virial for
backwards compatibility with codes written 30 years ago, but I could be wrong
here -- I'm not really sure how the MC barostat works. Basically, I think
we have all these checks and atom-reorderings to deal with a problem that
really doesn't exist....]


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Received on Thu Aug 06 2020 - 14:00:02 PDT
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