[gmx-users] trjconv mismatch

[Jennifer Vo]

Dear Mark,
Many thanks for your reply.
My command was:

trjconv_mpi -f md-*.trr -n index.ndx -timestep 100 -o md-*-timestep100.xtc

for every trr file, then concatenate by using

trjcat_mpi -f md-*-timestep100.xtc -n index.ndx  -o md-timestep100.xtc

For index.ndx:
make_ndx_mpi -f md.gro -o  index.ndx
and chose #1 for Protein.

Many thanks for any help!
Regards,
Jennifer


On Wed, Jan 14, 2015 at 9:09 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> On Wed, Jan 14, 2015 at 9:00 AM, Jennifer Vo <quyviolet at gmail.com> wrote:
>
> > Dear All,
> > I have got this error while running trjconv from .xtc to .pdb file. The
> > System includes 8 Protein (4622 Atoms each, x8 = 36976 Atoms). 135978 is
> > the total number of Atoms in the System. The index.ndx was created from
> > md.gro file, and I Chose #1 for Protein. I don't know where is the
> original
> > error of the mismatch here
> > 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 would appreciate for any help.
> >
>
> Providing your actual command lines and interactive choices would help. If
> you'd done the right things, you'd probably not be having a problem, so
> we'll need to know what things you actually did. ;-)
>
> Also, use gmx check on the .xtc and .tpr files, and less on the .ndx files
> to see whether these files contain the things you think they do.
>
> Mark
>
> Jennifer.
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