Generating a gromacs topology file for analyzing NAMD trajectories

From: patrick wintrode (
Date: Wed Dec 05 2007 - 14:15:11 CST


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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