From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Dec 19 2011 - 11:59:35 CST
On Mon, Dec 19, 2011 at 1:32 AM, rajitha tatikonda
> 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.
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.
> Ph.D student
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA.
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