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

[spss4 at iacs.res.in]

  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> -----