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

Marcelo Depólo marcelodepolo at gmail.com
Thu Aug 20 18:12:03 CEST 2015


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.

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

Does anyone have an idea about it?
Marcelo Depólo Polêto
Group of Structural Bioinformatics - Center of Biotechnology
Student of MSc Cell and Molecular Biology - UFRGS (Brazil)
B.Sc. Biochemistry - University of Viçosa (Brazil)

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