From: Daniel Roe <>
Date: Tue, 26 Apr 2016 09:14:35 -0600


This error message is pretty informative. Parmed is just letting you
know that even though you fixed your topology, any trajectories that
you've generated with the out of order topology no longer match. The
problem is you originally had some ordering like this:


So all trajectories you generated have the ordering A-C-B. When you
use parmed to fix the ordering in the topology to A-B-C, the ordering
in your trajectories is still A-C-B.

The solution is to use cpptraj and the 'fixatomorder' command to
reorder both topology and trajectories:

parm my.parm7
trajin min1.crd
fixatomorder outprefix reorder

You will get a re-ordered topology (my.parm7) and re-ordered
trajectory (

In the future it's usually a good idea to use parmed to check your
topology immediately after it is generated by leap.


On Tue, Apr 26, 2016 at 8:44 AM, Sanjib Paul <> wrote:
> Hii,
> I am trying to run, but I am getting some error like
> following
> *Atom 4074 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*
> So I have tried to fix it by In I am getting following
> messages*.*
> *> my.prmtop*
> *Loaded Amber topology file my.prmtopReading input from STDIN...*
>> setMolecules
> Setting MOLECULE properties of the prmtop (SOLVENT_POINTERS and
> MoleculeWarning: Molecule atoms are not contiguous! I am attempting to
> reorder the atoms to fix this.
> ParmWarning: The atoms in my.prmtop were reordered to correct molecule
> ordering. Any topology printed from now on will *not* work with the
> original inpcrd or trajectory files created with this prmtop! Consider
> quitting and loading a restart prior to using setMolecules
> I don't know what to do next. How will I get a correct prmtop file from
> Is it possible to change the corresponding inpcrd or rst file so
> that I can produce trajectory from them. Please help.
> Thanks and Regards.
> Sanjib Paul
> Indian Institute of Technology, Kharagpur
> India
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Apr 26 2016 - 08:30:03 PDT
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