[AMBER] cpptraj Error: Atom was assigned a lower molecule # than previous atom

From: Oliver Grant <olivercgrant.gmail.com>
Date: Fri, 19 Sep 2014 14:12:20 +0100

Hi all, I have a 6 domain protein which I have truncated to contain 11,746
atoms in 761 residues. There are a few amino acids missing beginning at
residue 248 so I've put capping groups at either end of the gap. All works
fine until I try to bond Cyx residues from different domains. tleap does
not complain but when I try to use the resulting topology file in cpptraj I
"*Error: Atom 3796 was assigned a lower molecule # than previous atom.*"
Atom 3796 is in residue 250, just after the missing loop. I guess tleap is
bonding the inter-domain Cyx residues and then assigning molecule numbers
based on which residues are connected together.

This is a problem when I try to autoimage with the resulting topology file
as cpptraj claims the file does not contain molecule information.

A similar problem was encountered previously and the cpptraj developer
Daniel Roe was working on a fix:

I'm using ambertools 14 built in April 2014. If a fix has become available
please let me know how to use it. I can "cheat" by not bonding the
inter-domain Cyx residues in tleap. This provides a topology file that
allows me to image my trajectories.

tleap bond commands which cause the problem to occur:
bond mol.157.SG mol.395.SG
bond mol.380.SG mol.619.SG
bond mol.604.SG mol.172.SG

Command used after tleap and error:
cpptraj -p CPLX_Neut_Sol.prmtop -i ptraj.in

CPPTRAJ: Trajectory Analysis. V14.00
    ___ ___ ___ ___
     | \/ | \/ | \/ |
Reading 'CPLX_Neut_Sol.prmtop' as Amber Topology
Error: Atom 3796 was assigned a lower molecule # than previous atom. This
Error: happen if 1) bond information is incorrect or missing, or 2) if the
Error: atom numbering in molecules is not sequential. If topology did not
Error: originally contain bond info, 1) can potentially be fixed by
Error: increasing the bondsearch cutoff offset (currently 0.200). 2) can
Error: fixed by either using the 'fixatomorder' command, or using
Error: the 'setMolecules' command in parmed.py.
Error: Could not determine molecule information for CPLX_Neut_Sol.prmtop.
Error: SetSolventInfo: No molecule information.
Error: Could not determine solvent information for CPLX_Neut_Sol.prmtop.
INPUT: Reading Input from file ptraj.in
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Received on Fri Sep 19 2014 - 06:30:03 PDT
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