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Department of Physics, University of Alberta
Edmonton CANADA
#
# Input parameters for mm_pbsa.pl
#
# Holger Gohlke
# 08.01.2002
#
##############################################################################
##
.GENERAL
#
# General parameters
# 0: means NO; >0: means YES
#
# mm_pbsa allows to calculate (absolute) free energies for one molecular
# species or a free energy difference according to:
#
# Receptor + Ligand = Complex,
# DeltaG = G(Complex) - G(Receptor) - G(Ligand).
#
# PREFIX - To the prefix, "{_com, _rec, _lig}.crd.Number" is added during
# generation of snapshots as well as during mm_pbsa calculations.
# PATH - Specifies the location where to store or get snapshots.
#
# COMPLEX - Set to 1 if free energy difference is calculated.
# RECEPTOR - Set to 1 if either (absolute) free energy or free energy
# difference are calculated.
# LIGAND - Set to 1 if free energy difference is calculated.
#
# COMPT - parmtop file for the complex (not necessary for option GC).
# RECPT - parmtop file for the receptor (not necessary for option GC).
# LIGPT - parmtop file for the ligand (not necessary for option GC).
#
# GC - Snapshots are generated from trajectories (see below).
# AS - Residues are mutated during generation of snapshots from trajectories.
# DC - Decompose the free energies into individual contributions
# (only works with MM and GB).
#
# MM - Calculation of gas phase energies using sander.
# GB - Calculation of desolvation free energies using the GB models in sander
# (see below).
# PB - Calculation of desolvation free energies using delphi (see below).
# 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 d01
PATH ./
#
COMPLEX 0
RECEPTOR 1
LIGAND 0
#
COMPT XXX
RECPT ../../myleapdir/d01.top
LIGPT XXX
#
GC 1
AS 0
DC 0
#
MM 0
GB 1
PB 1
MS 1
#
NM 0
#
##############################################################################
##
.PB
#
# PB parameters (this section is only relevant if PB = 1 above)
#
# The following parameters are passed to the PB solver.
# Additional parameters (e.g. SALT) may be added here.
# For further details see the delphi and pbsa documentation.
#
# PROC - Determines which method is used for solving the PB equation:
# If PROC = 1, the delphi program is applied. If PROC = 2,
# the pbsa program of the AMBER suite is used.
# REFE - Determines which reference state is taken for PB calc:
# If REFE = 0, reaction field energy is calculated with EXDI/INDI.
# Here, INDI must agree with DIELC from MM part.
# If REFE > 0 && INDI > 1.0, the difference of total energies for
# combinations EXDI,INDI and 1.0,INDI is calculated.
# The electrostatic contribution is NOT taken from sander here.
# INDI - Dielectric constant for the molecule.
# EXDI - Dielectric constant for the surrounding solvent.
# SCALE - Lattice spacing in no. of grids per Angstrom.
# LINIT - No. of iterations with linear PB equation.
# PRBRAD - Solvent probe radius in A (e.g. use 1.4 with the PARSE parameter se
t
# and 1.6 with the radii optimized by R. Luo)
#
# Parameters for pbsa only
#
# RADIOPT - Option to set up atomic avity radii for molecular surface calculat
ion
# and dielectric assignment. A value of 0 uses the cavity radii from the prm
top file.
# A value of 1 sets up optimized cavity radii at the pbsa initialization pha
se.
# The latter radii are optimized for model compounds of proteins only; use c
autions
# when applying these radii to nucleic acids.
#
# Parameters for delphi only
#
# FOCUS - If FOCUS > 0, subsequent (multiple) PERFIL and SCALE parameters are
# used for multiple delphi calculations using the focussing technique.
# The # of _focussing_ delphi calculations thus equals the value of FOCUS.
# PERFIL - Percentage of the lattice that the largest linear dimension of the
# molecule will fill.
# CHARGE - Name of the charge file.
# SIZE - Name of the size (radii) file.
#
# SURFTEN / SURFOFF - Values used to compute the nonpolar contribution Gnp to
# the desolvation according to Gnp = SURFTEN * SASA + SURFOFF.
#
#
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2.0
LINIT 500
PRBRAD 1.6
#
RADIOPT 0
#
FOCUS 0
PERFIL 80.0
CHARGE ./my_amber94_delphi.crg
SIZE ./my_parse_delphi.siz
#
SURFTEN 0.005
SURFOFF 0.0
#
##############################################################################
##
.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 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
##############################################################################
##
.MS
#
# Molsurf parameters (this section is only relevant if MS = 1 above)
#
# PROBE - Radius of the probe sphere used to calculate the SAS.
# Since Bondi radii are already augmented by 1.4A, PROBE should be 0.0
#
PROBE 0.0
#
##############################################################################
##
.MAKECRD
#
# The following parameters are passed to make_crd_hg, which extracts snapshots
# from trajectory files. (This section is only relevant if GC = 1 OR AS = 1 ab
ove.)
#
# BOX - "YES" means that periodic boundary conditions were used during MD
# simulation and that box information has been printed in the
# trajecotry files; "NO" means opposite.
# NTOTAL - Total number of atoms per snapshot printed in the trajectory file
# (including water, ions, ...).
# NSTART - Start structure extraction from NSTART snapshot.
# NSTOP - Stop structure extraction at NSTOP snapshot.
# NFREQ - Every NFREQ structure will be extracted from the trajectory.
#
# NUMBER_LIG_GROUPS - Number of subsequent LSTART/LSTOP combinations to
# extract atoms belonging to the ligand.
# LSTART - Number of first ligand atom in the trajectory entry.
# LSTOP - Number of last ligand atom in the trajectory entry.
# NUMBER_REC_GROUPS - Number of subsequent RSTART/RSTOP combinations to
# extract atoms belonging to the receptor.
# RSTART - Number of first receptor atom in the trajectory entry.
# RSTOP - Number of last receptor atom in the trajectory entry.
# Note: If only one molecular species is extracted, use only the receptor
# parameters (NUMBER_REC_GROUPS, RSTART, RSTOP).
#
BOX YES
NTOTAL 51
NSTART 1
NSTOP 300
NFREQ 100
#
NUMBER_LIG_GROUPS 0
#LSTART 52
#LSTOP 54
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 51
#
##############################################################################
##
#
.TRAJECTORY
#
# Trajectory names
#
# The following trajectories are used to extract snapshots with "make_crd_hg":
# Each trajectory name must be preceeded by the TRAJECTORY card.
# Subsequent trajectories are considered together; trajectories may be
# in ascii as well as in .gz format.
# To be able to identify the title line, it must be identical in all files.
#
TRAJECTORY ../../d01/strip.traj
#
##############################################################################
##
#
.PROGRAMS
#
# Program executables
#
#DELPHI /home/gohlke/src/delphi.98/exe/delphi
#
##############################################################################
##
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Received on Wed Nov 01 2006 - 06:07:35 PST