Re: MMPBSA-like analysis

From: Jason Swails (jason.swails_at_gmail.com)
Date: Tue Oct 22 2013 - 05:01:32 CDT

On Tue, Oct 22, 2013 at 5:21 AM, Peter Jones <pm-jones_at_bigpond.com> 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

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher

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