Re: MMPBSA-like analysis

From: Jason Swails (
Date: Tue Oct 22 2013 - 05:01:32 CDT

On Tue, Oct 22, 2013 at 5:21 AM, Peter Jones <> wrote:

> Dear Rethvi,
> I did this by converting the NAMD-generated dcd trajectory to AMBER format
> using the software Simulaid. Then you just prepare the appropriate AMBER
> topology and parameter files, and use the AMBER MM/PBSA protocols to
> analyse your trajectory. There might be issues here regarding artefacts or
> inaccuracies due to differences in the forcefields, I couldn't comment on
> that, but the results I got made very good sense. Converting the trajectory
> was no laughing matter either, and whichever way you go you're probably
> going to have to just dig into the errors until you get rid of them,

For what it's worth, the AmberTools program that performs MM/PBSA analyses
can read DCD files natively, so there's no need to convert them. The
tricky part is getting the topology file if you are starting with
CHARMM-based files.

Hope this helps,

Jason M. Swails
Rutgers University
Postdoctoral Researcher

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:48 CST