[gmx-users] cannot load the xtc file (without PBC) to VMD

[Lalehan Ozalp]

Thank you, but I haven't tried with a trr file and actually the last .trr
file I've produced is em.trr.
Thanks,

On Mon, Jan 13, 2020 at 5:40 PM <spss4 at iacs.res.in> wrote:

>   Hii
> Have you tried with the .trr file? Try the same procedure with .trr file.
> Thanks
> ----- Message from Lalehan Ozalp <lalehan.ozalp at gmail.com> ---------
>     Date: Mon, 13 Jan 2020 13:35:01 +0300
>     From: Lalehan Ozalp <lalehan.ozalp at gmail.com>
> Reply-To: gmx-users at gromacs.org
> Subject: [gmx-users] cannot load the xtc file (without PBC) to VMD
>       To: gmx-users at gromacs.org
>
> > Dear all, I have a question regarding loading .xtc file (with no periodic
> > boundary conditions) to VMD which I generated before. To this end, I had
> > used the command:
> > trjconv -f md_0_10.xtc -s md_30.tpr -n index.ndx -o noPBC.xtc -pbc mol
> -ur
> > compact -center
> > and selected *protein* for centering, and *system* for output.
> > However, when I load my corresponding gro file to VMD, and then loading
> the
> > xtc file above, the following error occurs:
> >
> > ERROR) BaseMolecule: attempt to init atoms while structure building in
> > progress!
> > ERROR) Invalid number of atoms in file: 132259
> > Info) Using plugin xtc for coordinates from file
> > /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc
> > ERROR) Incorrect number of atoms (132259) in
> > ERROR) coordinate file
> /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc
> > ERROR) Mismatch between existing molecule or structure file atom count
> and
> > coordinate or trajectory file atom count.
> > Info) Finished with coordinate file
> > /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc.
> >
> > This is especially strange since I carried out the same procedure several
> > times before. Additionally, I have a parallel system (with an isoenzyme
> of
> > the enzyme used here, with the same cofactor and the same ligand) and the
> > same steps worked perfectly. As a side note, this happens when I load xtc
> > file without PBC, while does not happen when I load xtc file in the
> > presence of PBC.
> >
> > Thank you so much in advance!
> > Lalehan
> > --
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> ----- End message from Lalehan Ozalp <lalehan.ozalp at gmail.com> -----
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