RE: Generating a gromacs topology file for analyzing NAMD trajectories

From: Xu, Jiancong (
Date: Thu Dec 06 2007 - 09:41:22 CST

In many cases with Gromacs analysis commands, you can use pdb file instead of .top file. And it works for PCA analysis as well.


Jiancong Xu, Ph.D.
Center for Molecular Biophysics
 Building 5700 MS6164
Oak Ridge National Laboratory
P.O.Box 2008
Oak Ridge TN 37830, USA.
Tel: (865) 241-1537

-----Original Message-----
From: on behalf of patrick wintrode
Sent: Wed 12/5/2007 3:15 PM
Subject: namd-l: Generating a gromacs topology file for analyzing NAMD trajectories

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?


Patrick L. Wintrode
Dept. of Physiology & Biophysics
Case Western Reserve University
Cleveland, OH 44106

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