Re: [AMBER] MMGBSA calculation gives very high positive free energy of binding!!!

From: David A Case <>
Date: Thu, 11 Jan 2018 07:38:49 -0500

On Thu, Jan 11, 2018, Sandip Mondal wrote:

> I am a beginner of MMGBSA calculation. I tried to calculate the
> binding free energy between protein and DNA in one protein-DNA
> complex using MMGBSA method as implemented in Amber14. I have
> performed molecular dynamics simulation by NAMD using charmm
> force field. From there I have taken equilibrated trajectory
> for the analysis. So, in order to run MMGBSA script using NAMD
> generated files, I need the corresponding Amber topology files
> (.prmtop file) for complex (protein-DNA), receptor (protein), and
> ligand (DNA) seperately. Then I prepared the necessary .prmtop
> file by using CHAMBER tool. Here I used top_all27_prot_na.rtf and
> par_all27_prot_na.prm as topology and parameter files respectively
> (for protein as well as DNA) for the preparation of .prmtop files
> using CHAMBER conversion tool. After the preparation of all required
> files, I run MMGBSA script.
> In the result part for multiple trajectory method, I got very very
> high positive free energy change of binding between protein and
> DNA. One more thing, the bonded terms (bond, angle, dihedral) in the
> MMGBSA method shows very high value with respect to the bonded terms
> of NAMD log file.

You need to establish first that the energies for individual snapshots that
you get with the chamber-generated tool match those you would get with NAMD
for the same coordinates. It sounds like looking at the bonded terms would
yield differences. Until you are sure you are getting correct energies for a
single snapshot, it doesn't make much sense to run the complete script.

Are you using the chamber option in parmed, or the old stand-alone "chamber"
program? The former has replaced the latter, and should be more reliable.


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Received on Thu Jan 11 2018 - 05:00:04 PST
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