[gmx-users] Re: problem in running grompp

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 10 12:39:41 CEST 2009

Samik Bhattacharya wrote:
> hi, i am simulating a membrane protein inside dppc bilayer and in this 
> regard i am following justin's tutorial. but i ma facing a problem in 
> running grompp...whenever i run it is giving error
> Program grompp, VERSION 4.0.5
> Source code file: grompp.c, line: 362
> Fatal error:
> number of coordinates in coordinate file (1A68_genbox.gro, 49128)
>              does not match topology (1A68.top, 48628)
> now how to solve this problem? i have first generated the lipid box  
> with the protein then solvated it. i really need little bit of help to 
> proceed to the next step...

The answer to this question is always the same.  You did not correctly update 
your topology after some preparation step.  You are off by 500 atoms, which, if 
you are using DPPC like the tutorial, corresponds to 10 lipids.  Look at what 
you've done carefully.


> Thaking You...
> Shamik
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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