[gmx-users] Converting pdb to tpr

X.Periole X.Periole at rug.nl
Mon Jul 24 11:50:33 CEST 2006

On Mon, 24 Jul 2006 09:50:09 +0100
  Samantha Kaye <samantha.kaye at bioch.ox.ac.uk> wrote:
> Hi,
> I found a thread on the gmx-users mailing list that said 
>using pdb2gmx will allow you to convert a pdb file to a 
>tpr file. However, when I use pdb2gmx -h I cannot see 
>which option will allow me to do this. Can someone tell 
>me please?

You might want to go through the gmx tutorial. All the 
to get from a pdb to tpr file and then an MD simulation
are introduced.

In brief the function pdb2gmx is to generate a topology
file (topol.top) of your system, e.g. protein, then you
would solvate your system, and finally use grompp together
with a coordinate file, a topology and a file containing 
way you want to simulate (mdp file) ... then you'll run.

pdb2gmx does not generate a tpr file !!


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