[gmx-users] Re: Require help in GROMACS

Justin A. Lemkul jalemkul at vt.edu
Tue May 12 16:02:31 CEST 2009

It would be best to post this message on the gmx-users list.  It is a 
Gromacs-related error message, and not specific to my tutorial.

It is an oft-encountered error, resulting from incorrect updating of your 
topology.  InflateGRO *did* remove lipids; check the screen output carefully. 
Here's how to tell:

grep POPC system_2.gro | wc -l

POPC molecules contain 52 atoms each, so 14716/52 = 283.  InflateGRO has 
apparently removed 5 lipids from your original 288.


Anirban Ghosh wrote:
> Respected Sir,
> I am trying to simulate a protein embeded in a POPC bilayer. As directed 
> by you I have followed your tutorial for this. But when executing the 
> command grompp for generating the .tpr for EM, I am getting the error:
> -------------------------------------------------------------------------------
> Fatal error:
> number of coordinates in coordinate file (system_2.gro, 18636)
>              does not match topology (topol.top, 18896)
> --------------------------------------------------------------------------------
> However while using InflateGRO, no lipid molecules were deleted. I am 
> attaching the files. Please have a look at them and advice. I could not 
> upload the files at the Gromacs mail list, so am writing to your 
> personal id. Please advice.
> Regards,
> -- 
> Anirban Ghosh


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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