[gmx-users] Can't load converted trajectory on to vmd

Seera Suryanarayana palusoori at gmail.com
Tue May 12 10:32:09 CEST 2015

Dear gromacs users
I have executed the trjconv command for generating the .xtc file to futher
analysis.  I have selected protein for output. I loaded the .gro file on to
vmd  and then I tried to load .xtc file on to vmd. But, I couldn't load it
and I got the following error.

vmd > Info) Using plugin gro for structure file
Info) Using plugin gro for coordinates from file
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info)    Atoms: 35183
Info)    Bonds: 24477
Info)    Angles: 0  Dihedrals: 0  Impropers: 0  Cross-terms: 0
Info)    Bondtypes: 0  Angletypes: 0  Dihedraltypes: 0  Impropertypes: 0
Info)    Residues: 10932
Info)    Waters: 10738
Info)    Segments: 1
Info)    Fragments: 10742   Protein: 1   Nucleic: 0
Info) Finished with coordinate file
ERROR) BaseMolecule: attempt to init atoms while structure building in
ERROR) Invalid number of atoms in file: 2966
Info) Using plugin xtc for coordinates from file
ERROR) Incorrect number of atoms (2966) in
ERROR) coordinate file
Info) Finished with coordinate file

Based on above information what I understood is that the .gro file has
35183 atoms including solvent atoms. But in .xtc file has only protein
atoms as I have selected protein as output during trjconv execution.
Actually I want to load only protein molecule on to vmd after mdrun. Kindly
tell me how to overcome this problem.

Thanks in Advance
Graduate student

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