VMD-L Mailing List

From: Seera Suryanarayana (palusoori_at_gmail.com)
Date: Tue May 12 2015 - 03:34:21 CDT

Dear vmd users

I have executed the trjconv command for generating the .xtc file to futher
analysis in gromacs. 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
/Extended/Dynamics/Hub_simulation/Gpu_md/1ycs/500ns/tmp/md_0_1.gro
Info) Using plugin gro for coordinates from file
/Extended/Dynamics/Hub_simulation/Gpu_md/1ycs/500ns/tmp/md_0_1.gro
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
/Extended/Dynamics/Hub_simulation/Gpu_md/1ycs/500ns/tmp/md_0_1.gro.
ERROR) BaseMolecule: attempt to init atoms while structure building in
progress!
ERROR) Invalid number of atoms in file: 2966
Info) Using plugin xtc for coordinates from file
/Extended/Dynamics/Hub_simulation/Gpu_md/1ycs/500ns/tmp/md_0_1_noPBC.xtc
ERROR) Incorrect number of atoms (2966) in
ERROR) coordinate file
/Extended/Dynamics/Hub_simulation/Gpu_md/1ycs/500ns/tmp/md_0_1_noPBC.xtc
Info) Finished with coordinate file
/Extended/Dynamics/Hub_simulation/Gpu_md/1ycs/500ns/tmp/md_0_1_noPBC.xtc.
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.

Surya
Graduate student
India.