MMPBSA Energy Calculations using VMD (Post-Processing)

From: Aditya Ranganathan (
Date: Thu Apr 10 2014 - 08:25:41 CDT

Dear All,

In order to study the allostery of a protein system, we performed targeted
molecular dynamics simulations using NAMD. We would now like to study the
conformational free energy landscape of the protein using MMPBSA. However,
the only one that we could find was the script in AMBERTOOLS 13.

Unfortunately, after a lot of attempts, we have still not been able to
successfully run the calculations owing to some repeated format errors
(CHARMM/XPLOR psf to AMBER prmtop). I would like to know if there are any
MMPBSA post-processing scripts (in VMD or otherwise) that have been
implemented to work with NAMD trajectories?

Any help from the community on this would be greatly appreciated. Looking
forward to your inputs.


Srivastav Ranganathan
Research Scholar
IIT Bombay
Mumbai, India

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