MMPBSA-like analysis

From: Revthi Sanker (
Date: Tue Oct 22 2013 - 02:04:49 CDT

Dear all,
I am trying to estimate the binding energy of a protein-ligand system that
I have simulated using NAMD with CHARMM forcefield. I have come come across
MMPBSA and MMPBSA-like analysis all of which are based on AMBER
forcefield. I have also tried converting the charmm format to amber format
using the program CHAMBER, but I am getting errors in that as well. Is
there any methodology that uses CHARMM forcefield in NAMD for Binding
energy calculation without having to run simulations for protein, ligand
and protein-ligand complex separately? Kindly provide your valuable
suggestions on the same.

I am aware that the question I am posting has been reviewed may a times in
the mailing list but I was unable to get a concrete answer or methodology
on how to actually go about it. Kindly help me in this as I am beginner to
MD simulations.
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:*

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