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

[Lalehan Ozalp]

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