AMBER Archive (2009)

Subject: [AMBER] Question on ECAVITY term of MM_PBSA

From: Gianluca Degliesposti (gianlucad.news_at_gmail.com)
Date: Mon Sep 14 2009 - 10:28:12 CDT

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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