AMBER Archive (2006)Subject: AMBER: molsurf or LCPO method in MM_GB/SA?
From: tonglei (xbcdnana_at_gmail.com)
Date: Tue Apr 04 2006  20:25:37 CDT
Dear everyone:
I try to use MM_GB/SA to calculate th binding energy of
proteinpeptide complex
here ,in my input files, the MS and GBSA terms are both used to caculate
the nonpolar
contributions to the solvation free energy (MS=1, GBSA=1)
But ,when MS=1 , the method of MOLSURF is employed
GBSA=1 the method of LCPO is also used
I want to know, if the two terms are defined as MS=1 and GBSA =1 ,
which method are used to calcute the the nonpolar contributions to the
solvation free energy
Is this parameters sets reasonable?
or the two terms should be MS=0 GBSA=1, thus the two terms are
compatible with the same method of LCPO
MS  Calculation of nonpolar contributions to desolvation using molsurf
# (see below).
# If MS == 0, nonpolar contributions are calculated with the LCPO
method
# in sander.
# NM  Calculation of entropies with nmode.
#
PREFIX r
PATH ./snapshot5
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./mcom.prmtop
RECPT ./mapo.prmtop
LIGPT ./axin.prmtop
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 0
MS 1
NM 0
#
################################################################################
@MM
#
# MM parameters (this section is only relevant if MM = 1 above)
#
# The following parameters are passed to sander.
# For further details see the sander documentation.
#
# DIELC  Dielectricity constant for electrostatic interactions.
# Note: This is not related to GB calculations.
#
DIELC 1.0
#
################################################################################
@GB
#
# GB parameters (this section is only relevant if GB = 1 above)
#
# The first group of the following parameters are passed to sander.
# For further details see the sander documentation.
#
# IGB  Switches between Tsui's GB (1), Onufriev's GB (2, 5).
# GBSA  Switches between LCPO (1) and ICOSA (2) method for SASA calc.
# Decomposition only works with ICOSA.
# SALTCON  Concentration (in M) of 11 mobile counterions in solution.
# EXTDIEL  Dielectricity constant for the solvent.
# INTDIEL  Dielectricity constant for the solute
#
# SURFTEN / SURFOFF  Values used to compute the nonpolar contribution Gnp
to
# the desolvation according to Gnp = SURFTEN * SASA +
SURFOFF.
#
IGB 2
GBSA 1
SALTCON 0.1
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.005
SURFOFF 0.00
Thank you

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