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

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 7 17:00:17 CEST 2008

Omer Markovitch wrote:
> Hello,
> 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 wrongly?

Charge information is not stored in a .xtc file, so it is of course not written. 
  Normally .pdb files do not contain charges, either.  You could fake it by 
writing the charges in the occupancy field or something, taking the charges from 
your .top or .tpr, which is where they really reside.


> (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.
> http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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