AMBER Archive (2009)

Subject: Re: [AMBER] Question on ECAVITY term of MM_PBSA

From: Ray Luo (ray.luo_at_uci.edu)
Date: Mon Sep 21 2009 - 12:30:57 CDT

Dear Gianluca,

Thanks for your report. We are looking into this ...

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/
==========================================

Gianluca Degliesposti wrote:
> Dear Amber developers,
>
> I sent the following question (see below) some time ago but unfortunately I
> did not receive an answer. Using Amber10, it seems to me that by setting
> PB=1, GB=1 and MS=0 (i.e. not using Molsurf) the nonpolar contribution to
> solvation is not calculated correctly, resulting in very small numbers. The
> impression is that surface or ECAVITY terms are multiplied by 0.0072 twice.
> This do not happen using PB=1, GB=1, MS=1. By setting PB=1, GB=0, MS=0 the
> ECAVITY term is calculated correctly but the statistics.out file is not
> created. This happens both with my input file and the mm_pbsa tutorial in
> the Examples directory that calculates binding free energies.
>
> Could you please explain if I am doing wrong or if there is an inconsistency
> in the way PBSUR is calculated?
>
> Thank you very much again.
>
>
> Dear all,
>
> I am running binding free energy calculations of a ligand to a protein using
> MM_PBSA of amber10, patched to bugfix.24. I noticed unreasonable differences
> in running the calculations with molsurf (MS=1) or LCPO (MS=0). In the
> output file obtained with MolSurf (com,rec,lig_all.out) the surface area and
> ECAVITY terms coincide, while in the LCPO calculation the ECAVITY term is
> much lower and approximately divided by 0.008 (this reminds the 0.0072
> factor, although this factor changes at every snapshot). Then, when we go to
> the statistics.out file, the PBSUR term calculated with molsurf is
> reasonable, while the PBSUR term obtained with LCPO is very close to zero.
> My impression is that with LCPO the surface area is multiplied by 0.0072 (or
> something close to this value) twice, therefore resulting in PBSUR values
> close to zero for all the ligands I am working with. I did not see this with
> Amber9, where the MS and LCPO results are similar.
>
> Thank you very much in advance for your suggestions. The input file I am
> using follows.
>
> # Input parameters for mm_pbsa.pl
>
> @GENERAL
>
> PREFIX complex_mmd7
>
> PATH ./
>
> #
>
> COMPLEX 1
>
> RECEPTOR 1
>
> LIGAND 1
>
> #
>
> COMPT protein_ligand_nowat.top
>
> RECPT protein_nowat.top
>
> LIGPT ligand_nowat.top
>
> #
>
> GC 0
>
> AS 0
>
> DC 0
>
> #
>
> MM 1
>
> GB 1
>
> PB 1
>
> MS 1 (or 0 when using LCPO)
>
> NM 0
>
> #
>
> @GB
>
> IGB 1
>
> GBSA 1
>
> SALTCON 0.00
>
> EXTDIEL 80.0
>
> INTDIEL 1.0
>
> #
>
> SURFTEN 0.0072
>
> SURFOFF 0.00
>
> #
>
> ################################################################################
>
> @PB
>
> PROC 2
>
> REFE 0
>
> INDI 1.0
>
> EXDI 80.0
>
> SCALE 2
>
> LINIT 1000
>
> PRBRAD 1.4
>
> #
>
> RADIOPT 0
>
> NPOPT 1
>
> CAVITY_SURFTEN 0.0072
>
> CAVITY_OFFSET 0.00
>
> SURFTEN 0.0072
>
> SURFOFF 0.00
>
> ################################################################################
>
>
> @MM
>
> DIELC 1.0
>
> ################################################################################
>
> @MS
>
> PROBE 0.0
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber