[gmx-users] coordinates don't match
lovikamoudgil at gmail.com
Wed Aug 27 15:15:37 CEST 2014
Thanks Justin!!!! :)
On Wed, Aug 27, 2014 at 5:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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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