[gmx-users] trjconv - converting trajectory into a pdb

Omer Markovitch omermar at gmail.com
Tue Oct 7 16:42:57 CEST 2008

I have ran some MD with GROMACS v3.3.3, and used the command "trjconv -f
traj.xtc -o traj.pdb -s file.gro" to generate a pdb movie.
My simulation includes charged atoms in some residues, but the output pdb
does not seem to include the formal charge data.
My question is, is this a known issue (that GROMACS does not print the
charge info. in the pdb), or, perhaps, it is a symptom of something I did
(its not a big deal, but still - it would be nice to have this data directly
in the movie)
    Thank you for the help, Omer.

Koby Levy research group,
Weizmann Institute of Science.
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