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

[spss4 at iacs.res.in]

  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> -----