[AMBER] MMPBSA.py and S-S bonds between different chains

From: Sergey Samsonov <sergey.samsonov.ug.edu.pl>
Date: Tue, 12 Dec 2017 16:58:59 +0100

Dear AMBERs,

I'm encountering the issue previously discussed in
http://archive.ambermd.org/201510/0052.html and

The problem appears when I have CYX-CYX bonds between the residues from
different chains written into the topology and use MMPBSA.py. The error
from MMPBSA.py is the following:

"Error: Atom 2194 was assigned a lower molecule # than previous atom..."

As Dan proposes in the discussion related to the same issue and as it is
suggested in the error message explicitly, I have rewritten both my
trajectory and the topology using 'fixatomorder outprefix reordered'
using cpptraj script. It looks like the new trajectory and the new
topology work well together: for example, there is no more problem when
I use them to create a new pdb file (with ambpdb), which was problematic
instead for the originals before applying fixatomorder.

My question is: how do I change the topologies for complex, receptor and
ligand for MMPBSA calculations? Without fixing them I have this error now:


IOError: [Errno 2] No such file or directory:
Error occured on rank 0.

An another interesting thing is that the same topologies worked without
any issues when I used amber14 for them a couple of years ago. Now I'm
using amber16.

Thank you very much in advance and cheers,


Sergey Samsonov, PhD
Project Leader at Laboratory of Molecular Modeling,
Department of Theoretical Chemistry,
Faculty of Chemistry,
University of Gdansk
ul. Wita Stwosza 63
80-308 Gdansk, Poland
phone: +48 58 523 5166
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Received on Tue Dec 12 2017 - 08:00:02 PST
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