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
--
==
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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