Re: [AMBER] Electrostatic energy calculated by MD in MM/GBSA

From: Jason Swails <>
Date: Fri, 18 Jul 2014 13:45:00 -0700

On Jul 18, 2014, at 1:38 PM, menwer momo <> wrote:

> Thank you for your reply.
> Yes I am testing protein mutants on the same DNA, and the "free DNA" contribution are
> identical for every mutant system.

They won't be "identical" if you ran separate MD simulations for each mutant. But if they are very close, that's good enough. (If you just did alanine scanning, then they will all be identical.)

> I am know trying to explain how each mutant affected the binding free energy,
> For example when I mutated Thr to Ala the electrostatic energy as calculated by MD became more negative, which is opposite of what I expected, so should I interpret this change by saying that this mutation caused the favorable electrostatic energy to increase ?

Alanine does not have a polar side-chain. If the only information I had to go on was what you gave me, I would re-word your statement to say "this mutation reduced some unfavorable electrostatic interactions" rather than increasing favorable interactions.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Jul 18 2014 - 14:00:02 PDT
Custom Search