[gmx-users] Re: topology and coordinate file not matching after grompp

Justin Lemkul jalemkul at vt.edu
Wed Jul 31 17:10:30 CEST 2013

On 7/31/13 10:07 AM, chinnu657 wrote:
> Thanks Justin. So, I've understood how to calculate the number of
> coordinates. That in the topology file matches the amount I calculated (as
> per how you just taught me).
> I want to put 2 proteins in the same box. I did this by changing the
> topology files of the respective proteins to itp. Then a new top file was
> made in which the itp files were included. I pasted the contents earlier.
> After this, performed editconf separately on each .gro file and combined
> them together. then I solvated them. Right before neutralising using genion,
> while using grompp to get the tpr file is where the error about the mismatch
> happens.
> How can I solve this? I've tried making sure my topology file is updated at
> every stage.

The most common source of problem is water molecules not being accurately 
accounted for, but the difference cited in the error message is 20, so it's 
probably not the waters.  I can't tell based on the description exactly what you 
did.  As I said before, an exact sequence of commands (copied and pasted from 
the terminal) is helpful.  Concatenating coordinate files is precarious, as you 
have to conduct manual deletions of lines to "fix" them after combining them.



Justin A. Lemkul, Ph.D.
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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