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 - 20:28:32 CDT

Dear Gianluca,

Unfortunately we couldn't reproduce any of your three observations. Have
you applied the latest bugfixes? Can you reproduce the examples within
the mmpbsa directory? Please make sure you have compiled all other
programs in the Amber10 successfully. Also make sure you have completely
cleaned the working directories, i.e. no files from previous runs.

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
> _______________________________________________
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>
>

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