Re: Re: Generating .tpr file using NAMD files

From: Axel Kohlmeyer (
Date: Mon Dec 19 2011 - 11:59:35 CST

On Mon, Dec 19, 2011 at 1:32 AM, rajitha tatikonda
<> wrote:
> Hi,
> I have performed MD simulation for my system using NAMD and for analysis  i am intending to use gromacs analysis tools but as this require .trr and .tpr files, i could convert my .dcd file to .trr using cat dcd and i am unable to generate .tpr file. I have gone through namd mailing list but did not understand how it is to done .Any help will be highly appreciated.

since .tpr files are a Gromacs specific file format, i find it a bit odd
that you ask about them and look for help on the NAMD mailing list.

nevertheless, here is a way that may help you (or not).
the .tpr file *will* have to be generated by the grompp tool,
which in turn requires a topology or .top file. if you want to
only use the gromacs analysis tools, you may not need a
complete .top file, but something simpler, that can be created
from a .psf/.pdb file combo as you have for a NAMD simulation.

check out:

and make sure you use the latest patchlevel from my homepage,
as it contains important bugfixes.

other than that, you have to use gromacs tools, eg. pdb2gmx
to build a fully working .top file and then a .tpr file from it.

> Thankyou,
> Rajitha
> Ph.D student
> India

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.

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