Re: Namd and MM-PBSA

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Thu Apr 23 2009 - 12:22:34 CDT

Esteban,

If you are referring to the binding of a ligand and not protein-protein binding, then presently it is best to use NAMD for the calculation of *relative* free energies of binding using either Free Energy Perturbation (FEP) or Thermodynamic Integration (TI) in NAMD 2.7b1 with the following softcore parameters (prior to any individual refinement as needed, according to your system):

fepVdwLambdaEnd 1.0
fepElecLambdaStart 0.5
fepVdwShiftCoeff 5.0

It is perhaps more advisable to attempt absolute binding energy calculations using a WCA decomposition of the energy/interaction contributions which we will be looking at implementing into NAMD sometime this summer.

If you are referring to protein-protein binding, this is a conceptually similar but practically another matter ....

C.

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                          Voice: 217-244-1733
http://www.ks.uiuc.edu/~char              Fax:   217-244-6078
Esteban Gabriel Vega Hissi <egvega_at_gmail.com> writes:
> Date: Thu, 23 Apr 2009 12:42:49 -0300
> From: Esteban Gabriel Vega Hissi <egvega_at_gmail.com>
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: Namd and MM-PBSA
> Return-Path: char_at_halifax.ks.uiuc.edu
> Message-ID: <9818bb9c0904230842v5c3d68e4vb231be233c1db1d5_at_mail.gmail.com>
> X-Spam-Status: No, score=-1.2 required=5.0 tests=BAYES_00,HTML_10_20,
> 	HTML_MESSAGE autolearn=no version=3.1.7-0+tcb1
> 
> 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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