Re: TopoTools for tpr file

From: Jeffrey Potoff (
Date: Fri Sep 09 2011 - 11:09:22 CDT

You are better off writing the topology file by hand or at least start
with pdb2gmx, which you can then edit to be consistent with your gromacs
parameter files and input coordinates.

To get the TPR file you need something like this:
grompp -f myfile.mdp -c myinputcoords.gro -p -o myinput.tpr

Where myfile.mdp is the file analogous to the NAMD simulation input file
that sets the temperature, timestep, etc.

As Alex mentioned, this is really a gromacs problem, so you should post
on their mailing list.

On 9/9/2011 10:01 AM, Hasan haska wrote:
> Dear NAMD users,
> I loaded my .psf and then loaded .pdb file into psf in VMD then used
> the command “ topo writegmxtop” in tk console. I finally
> generated a .top file successfully. But how can I generate a gromacs
> tpr file using this .top file ? Can you please give me the information
> about generating tpr file ?
> Thanks a lot for your help.

Jeffrey J. Potoff
Associate Professor			  Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr			  Phone:(313)577-9357		
Detroit, MI 48202  	                  Fax:  (313)578-5815

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