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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Received on Mon Sep 21 2009 - 04:30:03 PDT
