#
# Input parameters for mm_pbsa.pl
#
# Holger Gohlke
# 25.02.2010
#
################################################################################
@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).
#
# VERBOSE - If set to 1, input and output files are not removed. This is useful for
# debugging purposes.
# PARALLEL - If set to values > 1, energy calculations for snapshots are done
# in parallel, using PARALLEL number of threads.
#
# 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.
# START - Specifies the first snapshot to be used in energy calculations (optional, defaults to 1).
# STOP - Specifies the last snapshot to be used in energy calculations (optional, defaults to 10e10).
# OFFSET - Specifies the offset between snapshots in energy calculations (optional, defaults to 1).
#
# 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).
# Calculation of nonpolar solvation free energies according to
# the INP option in pbsa (see below).
# MS - Calculation of nonpolar contributions to desolvation using molsurf
# (see below).
# If MS == 0 and GB == 1, nonpolar contributions are calculated with the
# LCPO method in sander.
# If MS == 0 and PB == 1, nonpolar contributions are calculated according
# the INP option in pbsa (see below).
# NM - Calculation of entropies with nmode.
#
VERBOSE 1
PARALLEL 0
#
PREFIX 1_1
PATH ./
START 1
STOP 100000
OFFSET 1
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT FABI_C01_ChainD_1.top
RECPT FABI_C01_ChainD.top
LIGPT 1.top
#
GC 0
AS 0
DC 1
#
MM 1
GB 1
PB 1
MS 0
#
NM 0
#
################################################################################
@DECOMP
#
# Energy decomposition parameters (this section is only relevant if DC = 1 above)
#
# Energy decomposition is performed for gasphase energies, desolvation free
# energies calculated with GB, and nonpolar contributions to desolvation
# using the ICOSA method.
# For amino acids, decomposition is also performed with respect to backbone
# and sidechain atoms.
#
# DCTYPE - Values of 1 or 2 yield a decomposition on a per-residue basis,
# values of 3 or 4 yield a decomposition on a pairwise per-residue
# basis. For the latter, so far the number of pairs must not
# exceed the number of residues in the molecule considered.
# Values 1 or 3 add 1-4 interactions to bond contributions.
# Values 2 or 4 add 1-4 interactions to either electrostatic or vdW
# contributions.
#
# COMREC - Residues belonging to the receptor molecule IN THE COMPLEX.
# COMLIG - Residues belonging to the ligand molecule IN THE COMPLEX.
# RECRES - Residues in the receptor molecule.
# LIGRES - Residues in the ligand molecule.
# {COM,REC,LIG}PRI - Residues considered for output.
# {REC,LIG}MAP - Residues in the complex which are equivalent to the residues
# in the receptor molecule or the ligand molecule.
#
DCTYPE 2
#
COMREC 1-259
COMLIG 260-260
COMPRI 1-260
RECRES 1-259
RECPRI 1-259
RECMAP 1-259
LIGRES 1-1
LIGPRI 1-1
LIGMAP 260-260
################################################################################
@PB
#
# PB parameters (this section is only relevant if PB = 1 above)
#
# The following parameters are passed to the PB solver.
# Additional input parameters may also be added here. See the sander PB
# documentation for more options.
#
# PROC - Determines which method is used for solving the PB equation:
# By default, PROC = 2, the pbsa program of the AMBER suite is used.
# REFE - Determines which reference state is taken for PB calc:
# By default, REFE = 0, reaction field energy is calculated with
# EXDI/INDI. Here, INDI must agree with DIELC from MM part.
# INDI - Dielectric constant for the solute.
# EXDI - Dielectric constant for the surrounding solvent.
# ISTRNG - Ionic strength (in mM) for the Poisson-Boltzmann solvent.
# PRBRAD - Solvent probe radius in Angstrom:
# 1.4: with the radii in the prmtop files. Default.
# 1.6: with the radii optimized by Tan and Luo (In preparation).
# See RADIOPT on how to choose a cavity radii set.
# RADIOPT - Option to set up radii for PB calc:
# 0: uses the radii from the prmtop file. Default.
# 1: uses the radii optimized by Tan and Luo (In preparation)
# with respect to the reaction field energies computed
# in the TIP3P explicit solvents. Note that optimized radii
# are based on AMBER atom types (upper case) and charges.
# Radii from the prmtop files are used if the atom types
# are defined by antechamber (lower case).
# SCALE - Lattice spacing in no. of grids per Angstrom.
# LINIT - No. of iterations with linear PB equation.
# IVCAP - If set to 1, a solvent sphere (specified by CUTCAP,XCAP,YCAP,
# and ZCAP) is excised from a box of water. If set to 5, a solvent shell
# is excised, specified by CUTCAP (the thickness of the shell in A).
# The electrostatic part
# of the solvation free energy is estimated from a linear response
# approximation using the explicit water plus a reaction field
# contribution from outside the sphere (i.e., a hybrid solvation approach
# is pursued). In addition, the nonpolar
# contribution is estimated from a sum of (attractive) dispersion
# interactions calc. between the solute and the solvent molecules
# plus a (repulsive) cavity contribution. For the latter,
# the surface calculation must be done with MS = 1 and the PROBE should
# be set to 1.4 to get the solvent excluded surface.
# CUTCAP - Radius of the water sphere or thickness of the water shell.
# Note that the sphere must enclose the whole solute.
# XCAP - Location of the center of the water sphere.
# YCAP
# ZCAP
#
# NP Parameters for nonpolar solvation energies if MS = 0
#
# INP - Option for modeling nonpolar solvation free energy.
# See sander PB documentation for more information on the
# implementations by Tan and Luo (In preparation).
# 1: uses the solvent-accessible-surface area to correlate total
# nonpolar solvation free energy:
# Gnp = SURFTEN * SASA + SURFOFF. Default.
# 2: uses the solvent-accessible-surface area to correlate the
# repulsive (cavity) term only, and uses a surface-integration
# approach to compute the attractive (dispersion) term:
# Gnp = Gdisp + Gcavity
# = Gdisp + SURFTEN * SASA + SURFOFF.
# When this option is used, RADIOPT has to be set to 1,
# i.e. the radii set optimized by Tan and Luo to mimic Gnp
# in TIP3P explicit solvents. Otherwise, there is no guarantee
# that Gnp matches that in explicit solvents.
# SURFTEN/SURFOFF - Values used to compute the nonpolar
# solvation free energy Gnp acccording to INP.
# If INP = 1 and RADIOPT = 0 (default, see above),
# use SURFTEN/SURFOFF parameters that fit with the radii from the
# prmtop file, e.g., use SURFTEN: 0.00542; SURFOFF: 0.92 for PARSE radii.
# If INP = 2 and RADIOPT = 1, these two lines
# can be removed, i.e. use the default values set in pbsa
# for this nonpolar solvation model. Otherwise, please
# set these to the following: SURFTEN: 0.04356; OFFSET: -1.008
#
# NP Parameters for nonpolar solvation energies if MS = 1
#
# SURFTEN/SURFOFF - Values used to compute the nonpolar contribution Gnp to
# the desolvation according to either
# (I) Gnp = SURFTEN * SASA + SURFOFF (if IVCAP = 0) or
# (II) Gnp = Gdisp + Gcavity = Gdisp + SURFTEN * SESA + SURFOFF (if IVCAP > 0).
# In the case of (I), use parameters that fit with the radii from the
# reaction field calculation. E.g., use SURFTEN: 0.00542, SURFOFF: 0.92
# for PARSE radii or use SURFTEN: 0.005, SURFOFF: 0.86 for Tan & Luo radii.
# In the case of (II), use SURFTEN: 0.069; SURFOFF: 0.00 for calculating the
# Gcavity contribution.
#
PROC 2
REFE 0
INDI 1
EXDI 80.0
SCALE 2
LINIT 1000
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 0
INP 0
#
SURFTEN 0.04356
SURFOFF -1.008
#
IVCAP 0
CUTCAP -1.0
XCAP 0.0
YCAP 0.0
ZCAP 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
#
################################################################################
@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) and 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 5
GBSA 2
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1
#
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.
# In general, since Bondi radii are already augmented by 1.4A,
# PROBE should be 0.0
# In IVCAP = 1 or 5, the solvent excluded surface is required for
# calculating the cavity contribution. Bondi radii are not
# augmented in this case and PROBE should be 1.4.
#
PROBE 0.0
#
#################################################################################
@NM
#
# Parameters for sander/nmode calculation (this section is only relevant if NM = 1 above)
#
# The following parameters are used for entropy calculation using
# gasphase statistical mechanics.
# For further details see documentation.
#
# PROC - Determines which method is used for the calculations:
# By default, PROC = 1, the NAB implementation of nmode is used.
# This allows using either a GB model or a distance-dependent dielectric
# for electrostatic energies. No entropy decomposition is possible, however.
# If PROC = 2, the "original" nmode implementation is used.
# Here, only a distance-dependent dielectric is avaliable for
# electrostatic energies. Entropy decomposition is possible here, too.
# MAXCYC - Maximum number of cycles of minimization.
# DRMS - Convergence criterion for the energy gradient.
# IGB - Switches between no GB (i.e., vacuum electrostatics) (0) or Tsui's GB (1).
# SALTCON - Concentration (in M) of 1-1 mobile counterions in solution.
# EXTDIEL - Dielectricity constant for the solvent.
# SURFTEN - Value used to compute the nonpolar contribution Gnp to
# the desolvation according to Gnp = SURFTEN * SASA.
# DIELC - (Distance-dependent) dielectric constant (if IGB = 0)
#
PROC 1
#
MAXCYC 10000
DRMS 0.5
#
IGB 1
SALTCON 0.00
EXTDIEL 80.0
SURFTEN 0.0072
#
DIELC 1
#
################################################################################
@PROGRAMS
#
# Additional program executables can be defined here
#
#
################################################################################