Dear AMBERs,
I'm encountering the issue previously discussed in
http://archive.ambermd.org/201510/0052.html and
http://archive.ambermd.org/201409/0451.html
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:
'_MMPBSA_complex_gb_surf.dat.0'
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
--
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
