[gmx-users] Getting error using gmx trjconv

[Justin Lemkul]

On 10/8/18 9:51 AM, Saikat Pal wrote:
> Dear all,I am getting this kind of error :
>
> Command line:
>    gmx trjconv -s 148d-wat-0-reduce-oct_GMX-1.gro -f b.tng -o c.tng -fit rot+trans -n test-o.ndx
>
> Will write tng: Trajectory file (tng format)
>
> WARNING: Masses and atomic (Van der Waals) radii will be guessed
>           based on residue and atom names, since they could not be
>           definitively assigned from the information in your input
>           files. These guessed numbers might deviate from the mass
>           and radius of the atom type. Please check the output
>           files if necessary.
>
>
> WARNING: If there are molecules in the input trajectory file
>           that are broken across periodic boundaries, they
>           cannot be made whole (or treated as whole) without
>           you providing a run input file.
>
> Select group for least squares fit
> Group     0 (            URE) has  4000 elements
> There is one group in the index
> Select group for output
> Group     0 (            URE) has  4000 elements
> There is one group in the index
> Reading frame       0 time 1035500.000
> Precision of b.tng is 0.001 (nm)
>
> -------------------------------------------------------
> Program:     gmx trjconv, version 2018.3
> Source file: src/gromacs/gmxana/gmx_trjconv.cpp (line 1350)
>
> Fatal error:
> Index[3498] 4001 is larger than the number of atoms in the
> trajectory file (4000). There is a mismatch in the contents
> of your -f, -s and/or -n files.
>

Looks like you've chosen to save fewer atoms in the trajectory than you 
have in your reference structure. The two need to match.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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