[gmx-users] Converting pdb to tpr

[Samantha Kaye]

That's what I thought.

I wanted to use g_hbond on frames of a trajectory that I have docked a ligand into to extract the contacts made. However, my initial tpr file doesn't have the ligand in as it was never there in the initial simulation. 

I'll just have to think of another way to look at the h-bonds.

Thanks 


In message <web-23801401 at mail3.rug.nl> Discussion list for GROMACS users <gmx-users at gromacs.org> writes:
> 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 
> steps
> 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 
> the
> way you want to simulate (mdp file) ... then you'll run.
> 
> pdb2gmx does not generate a tpr file !!
> 
> XAvier
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-- 
Samantha Kaye
Structural Bioinformatics and Computational Biochemistry Group
University of Oxford