[gmx-users] trjconv mismatch

[Tsjerk Wassenaar]

Hi Jennifer,

You can extract the first frame using the same logic and save it as
PDB/GRO. Then you can use that structure as reference for the second pass.
However, in this case it seems more logical to just write out a PDB
trajectory directly and use 'cat' to combine them in a single file.

Hope it helps,

Tsjerk

On Wed, Jan 14, 2015 at 10:07 AM, Jennifer Vo <quyviolet at gmail.com> wrote:

> 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.
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
Tsjerk A. Wassenaar, Ph.D.