[gmx-developers] tpr format

[nmichaud at jhu.edu]

On Thu, 20 Apr 2006, Xavier Periole wrote:

> nmichaud at jhu.edu wrote:
>
> >Hello,
> >
> >Is the tpr format documented anywhere (besides the source). I would like
> >to use gromacs' geometric analysis tools for a simulation I did with
> >NAMD. The trajectory I can convert from dcd to xtc, (is there also
> >
> >
> vmd 1.8.4 can write trajectory in trr format !!

I don't believe that VMD can write trajectories in trr format. I wrote
code to convert my dcds to the xtc format to save space.


>
> >documentation for the trr/trj format), but require either a tpr, tpb
> >or tpa (what is the difference between all these?) for most of the
> >analysis tools.
> >
> >
> For many of the analysis tools you can use a coordinate file, either gro
> or pdb file.
> To get a tpr file is quite easy from a pdb file if your system is a
> protein. Adding
> solvent would more problematic, but feasible.
>
> pdb2gmx -f file.pdb gives you a topol.tpr that you can use.
>

Ah, so I have to go through gromacs. The problem is my system is
coarse-grained and as a result i wanted to create the tpr file by
hand, since I don't have an itp file that describes my system.

Naveen