I've done what you recommended, but I'm still getting the same set of errors. I also tried rebuilding my .prmtop file with tleap but I commented out the line where the heme and protein are bound together and I still get the same errors, including the one that says that atoms in the heme are in two residues. There was a little bit of processing done on the heme prior to this step, but it just involved removing an atom. I don't think this is causing the error, but I wanted to mention it in case it was relevant.
Thanks,
Sam
________________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Thursday, August 6, 2020 4:30 PM
To: AMBER Mailing List
Cc: amber-developers.ambermd.org
Subject: Re: [AMBER] Parmed: Residues cannot be part of 2 molecules! Molecule section will not be correctly set.
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....]
...dac
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Received on Fri Aug 07 2020 - 09:00:02 PDT
