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

From: Jason Swails <>
Date: Fri, 7 Aug 2020 22:13:29 -0400

> On Aug 7, 2020, at 2:52 PM, Daniel Roe <> wrote:
> 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.

This was definitely true before I went to my current job in 2016, but I’m pretty sure that code hasn’t changed in the last 4 years (it hadn’t in well over a decade prior).

AMBER-Developers mailing list
Received on Fri Aug 07 2020 - 19:30:02 PDT
Custom Search