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

[Lalehan Ozalp]

Hey again, sorry for the late reply. I meant, I didn't have the chance to
do that since a .trr file after the simulation was not generated. All I had
was the em.trr. Later, I solved the problem by using editconf. Thank you
for your attention.

On Tue, Jan 14, 2020 at 2:51 PM <spss4 at iacs.res.in> wrote:

>   I didn't get you. So your problem is solved using trr file or not?
> ----- Message from Lalehan Ozalp <lalehan.ozalp at gmail.com> ---------
>     Date: Tue, 14 Jan 2020 12:53:54 +0300
>     From: Lalehan Ozalp <lalehan.ozalp at gmail.com>
> Reply-To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] cannot load the xtc file (without PBC) to VMD
>       To: gmx-users at gromacs.org
>
> > 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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> ----- End message from Lalehan Ozalp <lalehan.ozalp at gmail.com> -----
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