From: Jeffrey Potoff (jpotoff_at_chem1.eng.wayne.edu)
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 topol.top -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.
J-
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 myfile.top” 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 jpotoff_at_chem1.eng.wayne.edu 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 http://potoff1.eng.wayne.edu ======================================================================
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