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

From: Daniel Roe <>
Date: Fri, 7 Aug 2020 14:52:02 -0400

On Thu, Aug 6, 2020 at 4:30 PM David A Case <> wrote:
> [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....]

In order to do things like by-molecule imaging, cpptraj assumes
molecules are contiguous. If they are not, all molecule-related stuff
(imaging by molecule, 'closest', etc) is disabled. I suspect the
molecule "wrapping" code in sander/pmemd might make this assumption as
well, but I'm not sure.


> ...dac
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Received on Fri Aug 07 2020 - 12:00:03 PDT
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