Re: MMPBSA-like analysis

From: Revthi Sanker (
Date: Tue Oct 22 2013 - 11:12:52 CDT

Dear Sir,
I did use the same dcd file as AMBER could read them and tried using the
CHAMBER- a module in AMBER that converts the charmm topology to AMBER
topology. That met with severe fortran errors and I am unable to rectify
them as I do not have much of a programming experience. Is there any tool
that would make this topology conversion possible?
Kindly provide your valuable suggestions in this regard.

Thank you for your help in advance.

M.S. Research Scholar
Indian Institute Of Technology, Madras
International Conference on Bimolecular Simulations and Dynamics
*Official website:*

On Tue, Oct 22, 2013 at 3:31 PM, Jason Swails <>wrote:

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

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