[gmx-users] coordinates don't match

Justin Lemkul jalemkul at vt.edu
Wed Aug 27 13:46:52 CEST 2014

On 8/27/14, 1:10 AM, Lovika Moudgil wrote:
> Hi everyone ,
> I have a question , If coordinates of my .pdb file and .top file are not
> matching than what is the right way to correct it ! Like if I have one
> coordinate more in .pdb than in .top and I delete one  from .pdb ...and it
> get fine !!! Will it be a problem in future or its fine to do this ?? Is
> there any other way to correct it ...without deleting !!

You shouldn't make manual modifications like this.  A difference of one atom is 
curious, and haphazard deletion of a single atom is very worrisome.  Likely 
grompp is complaining about other things like mismatching names, suggesting a 
serious disagreement between the coordinates and topology.  Gromacs tools 
(genbox, genion) modify the topology for you in cases of water and ions.  Any 
other modifications (ligands, etc) need to be handled carefully.  As a rule, if 
you change the contents of the coordinates in any way, stop and verify that the 
topology has been modified correctly before proceeding to the next step.

Without the full context of what you're doing and the exact sequence of 
commands, that's the best advice I can give.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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