Re: MMPBSA-like analysis

From: Peter Jones (
Date: Tue Oct 22 2013 - 04:21:24 CDT

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,

good luck,

Peter Jones

On 22/10/2013, at 6:04 PM, Revthi Sanker wrote:

> 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.
> Revathi.S
> M.S. Research Scholar
> Indian Institute Of Technology, Madras
> India
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