[gmx-users] Fatal error: Index contains atom numbers larger than the topology

Justin Lemkul jalemkul at vt.edu
Thu Aug 20 18:20:36 CEST 2015

On 8/20/15 12:12 PM, Marcelo Depólo wrote:
> Hi!
> I am running a DoS calculation using g_dos on 5.0.6 version, using the .tpr
> used to generate a .trr trajectory. Hence, the topology and index should
> contain the same number of atoms and I confirmed this by looking the number
> of atoms on the generated .gro.

This check tells you nothing of use.  A .gro will always have the whole system 
in it; there's no way to write out a subset of atoms here via mdrun.

> Still, I got the error:
> Command =
> *g_dos_506 -s ani.DOS.tpr -f ani.DOS.trr -beginfit 20 -endfit 40 -T 298
> -dos ani.dos.xvg*
> *Reading file ani.DOS.tpr, VERSION 5.0.6 (single precision)Reading file
> ani.DOS.tpr, VERSION 5.0.6 (single precision)Group     0 (         System)
> has 14000 elementsGroup     1 (          Other) has 14000 elementsGroup
> 2 (            ANI) has 14000 elementsSelect a group:
> 0-------------------------------------------------------Program g_dos_506,
> VERSION 5.0.6Fatal error:Index contains atom numbers larger than the
> topology*
> Does anyone have an idea about it?

What does gmxcheck tell you about all the files involved?  How did you generate 
the index file?  As the error says, the problem comes from the index file 
specifying something that doesn't exist in the topology.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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