[gmx-users] Index is larger than the number of atoms in the trajectory file

Justin Lemkul jalemkul at vt.edu
Tue Mar 21 13:19:29 CET 2017

On 3/20/17 4:24 PM, Mahboobeh Eslami wrote:
> Hi all GMX usersI hope you are wellI have simulated a protein-ligand complex. My protein has two calcium ions. I want to use GMXPBSA approach for free energy calculation.
> If I remove calcium ions,  I will get following error in the first step of MMPBSA calculation:Fatal error:
> Index[1673] 1676 is larger than the number of atoms in the
> trajectory file (1675). There is a mismatch in the contents
> of your -f, -s and/or -n files.How can I solve this problem. please guide me

You probably only saved a subset of the system when writing the trajectory, 
which is now out of sync with an index file that was presumably constructed from 
the whole system.  Re-create the index file or save corresponding groups when 
writing the trajectory.



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


More information about the gromacs.org_gmx-users mailing list