From: Axel Kohlmeyer (
Date: Tue Dec 27 2011 - 17:32:59 CST

On Tue, Dec 27, 2011 at 4:38 PM, J. Matthew Franklin <> wrote:
> Hi,
> I want to generate pdb files for every 100 frames of a simulation.
> I have the .xtc file for the simulation, but to my knowledge, this only
> contains coordinates and not enough information to generate a pdb.
> When I tried to "save coordinates" as a pdb in VMD, I got an error:
> Molecule's structure has not been intialized.
>  I'm guessing that I can load some other file with information about the
> element of each atom, etc?

yes. if do you have some pdb file of the same system,
you can just load that pdb and then just write out the
frames (best with a script). you can also script this
if needed (this is what the topotools plugin does,
for example when reading lammps data files or
.xyz files).


> Any help would be appreciated.
> Thanks,
> Matt

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.