Re: Namd and MM-PBSA

From: JT (jtibbitt_at_odu.edu)
Date: Thu Apr 23 2009 - 12:43:17 CDT

Esteban,
This requires calculating the free energy (G) three times:
Binding Energy = G(complex) - [G(protein) + G(ligand)].

The MMPBSA method for calculating a molecule's free energy is:
G = MM + PB + SA - TS.

NAMD (or its counterpart VMD) gives you the MM energy of the
molecule. APBS gives you the PB (and possibly SA) solvation energy.
VMD can calculate the surface area, so you can use it to get the SA
solvation energy. I'm not sure if NAMD calculates the surface area.
So all you need is the entropy. That requires either running NAMD
simulations of the 3 molecules, then obtaining the quasiharmonic
normal modes, or directly obtaining the classical normal modes of the
three molecules. Either way, you need to perform Normal Mode Analysis
to get at the mode frequencies, and NAMD does not do it. So it looks
like you need a 3 (or 4, if including VMD) programs. There are free
public Normal Mode Analysis web servers on the internet.

Jeff

On Apr 23, 2009, at 11:42 AM, Esteban Gabriel Vega Hissi wrote:

> Hi everyone,
> I found 2 old (2005 and 2006) and useless entries for the problem of
> calculation absolutes binding free energy and binding constants with
> MM-PBSA.
> I wonder how (most detailed as possible) can I calculate binding
> free energy ONLY using Namd and any PBS program (like APBS)?
>
> Thanks in Advance!
>
> Esteban G Vega H
> egvega_at_gmail.com
> FQByF
> Universidad Nacional de San Luis
> Argentina

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