Re: Generating a gromacs topology file for analyzing NAMD trajectories

From: L. Michel Espinoza-Fonseca (
Date: Wed Dec 05 2007 - 14:52:52 CST

Hi Patrick,

In order to perform PCA in gromacs starting from a DCD trajectory, you
just need a pdb file (that will be your input topology) that contains
exactly the same number of atoms as in your trajectory. This pdb file
could be that taken at t=0ns.

One more detail: you need to convert your DCD trajectory to a TRR one
before performing the actual PCA (you can do that easily with VMD). In
summary, for a standard PCA in gromacs you'll only need a pdb file
(the topology) and the trajectory (in TRR or XTC format).

That would be enough, I guess. Good luck!


On Dec 5, 2007 9:15 PM, patrick wintrode <> wrote:
> 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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