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
protein-peptide 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 1-1 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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