[gmx-users] trjconv mismatch in number of atoms

[Justin Lemkul]

On 1/13/15 10:15 AM, Jennifer Vo wrote:
> Dear Experts,
> I am running a trjconv from xtc files to pdb file but have got this error:
>
> Fatal error:
> Index[4622] 135978 is larger than the number of atoms in the
> trajectory file (36976). There is a mismatch in the contents
> of your -f, -s and/or -n files.
>
> I don't know where the origin of the Problem, the index.ndx was created
> from md.gro file, the *.xtc (8 Proteins in a box, so I type #1 to have the
> index of 8 Proteins, each Protein has 4622 Atoms). The trajectory has 36976
> Atoms which is 4622 * 8  and 135978 is the total number of Atoms in the

This means you chose "Protein" as the only group saved in the .xtc 
(xtc-grps/compressed-x-grps).  If you want to do analysis, you need to re-create 
your index file and perhaps make a matching .tpr file.

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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