Re: Generating a gromacs topology file for analyzing NAMD trajectories

From: Giovanni Bellesia (
Date: Wed Dec 05 2007 - 15:25:42 CST

I used once the GROMACS g_covar tool converting first my dcd file to
trr with catdcd and using a pdb file as the Structure+mass input file .
In details:

catdcd -o myfile.trr -otype trr myfile.dcd
g_covar -f myfile.trr -s mypdb.pdb

> Hi.
> I'm trying to use gromacs to do PCA on a trajectory I generated using
> NAMD. This requires a .top file.
> So far, I tried using 1 frame of my trajectory (saved as a pdb file) I
> aliased HSE back to HIS and ILE CD back to CD1. Nevertheless, the
> program pdb2gmx (for making gromacs files) keeps running into atom
> types that it can't recognize (this even happens when I use the
> "ignore hydrogens" option).
> I could start from the original pdb from the protein data bank, but
> wouldn't this generate a .top file that would be incompatible with the
> trajectory?
> Has anyone successfully used gromacs to do PCA of a NAMD trajectory?
> If so, how did you generate your .top file?
> Thanks.
> Patrick L. Wintrode
> Dept. of Physiology & Biophysics
> Case Western Reserve University
> Cleveland, OH 44106

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