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

From: Jason Swails <>
Date: Fri, 19 Sep 2014 09:29:55 -0400

On Fri, Sep 19, 2014 at 9:12 AM, Oliver Grant <>

> 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
> get:
> "*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
> 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
> can
> 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
> be
> Error: fixed by either using the 'fixatomorder' command, or using
> Error: the 'setMolecules' command in
> 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

​Try using the "fixatomorder" command at the beginning of your cpptraj
script. That should fix the molecule issue and allow you to image.

Note that you should write a new prmtop file since the atom ordering in
your system will change (and you will need this new prmtop file to analyze
any trajectory you print out after running fixatomorder).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Sep 19 2014 - 07:00:02 PDT
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