AMBER Archive (2009)

Subject: Re: [AMBER] problem of PBCAL/GB

From: Qinghua Liao (fantasticqhl_at_yahoo.com)
Date: Tue Sep 08 2009 - 04:40:42 CDT

Hi Prof. Ray Luo,

Thanks very much for your explanation! I think I understand a little now. Thanks!

All the best,

Qinghua

________________________________
From: Ray Luo <ray.luo_at_uci.edu>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Tuesday, September 8, 2009 1:58:44 PM
Subject: Re: [AMBER] problem of PBCAL/GB

Qinghua,

The positive number is for the delta PB, i.e. the solvation electrostatic interaction is against binding. Note too that delta EEL is negative, i.e. the intermolecular electrostatic interaction is for binding. These two components are always trying to cancel each other so the total delta energy is won't be that crazy in the end, as seen in experiment.

All the best,
Ray

==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

Qinghua Liao wrote:
> Dear amber users,
> In the course of mm_pbsa online, http://ambermd.org/tutorials/advanced/tutorial3, in the final results of mm_pbsa, the value of PBCAL is 944.49. Why is it positive? Is that right? While PBCAL/GB is explained as the electrostatic contribution to the solvation free energy calculated by PB or GB respectively. I am just confused, could somebody help me? Thanks in advance!
>  Best wishes!
>  Qinghua
>
>
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