[gmx-users] error with indexfile

Justin Lemkul jalemkul at vt.edu
Fri Jan 4 12:11:13 CET 2013

On 1/4/13 12:51 AM, Kieu Thu Nguyen wrote:
> Dear All,
> When using the command
> grompp -f equi.mdp -c membedded.gro -p merged.top -n index.ndx -o
> equilibrate.tpr
> The error is
> Fatal error:
> Invalid atom number 6518 in indexfile
> How can i fix this ?

Hard to say.  You haven't told us what's in the system, why you're using an 
index file, or how you created the index groups.  Basically, grompp is telling 
you that there are fewer atoms in the coordinate file than there are in the 
index file.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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