#
# 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).
#        Calculation of nonpolar solvation free energies according to
#        the NPOPT 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 NPOPT option in pbsa (see below).
#   NM - Calculation of entropies with nmode.
#
PREFIX                snapshot
PATH                  ./
#
COMPLEX               0
RECEPTOR              1
LIGAND                0
#
COMPT                 ./
RECPT                 ./vacuo.prmtop
LIGPT                 ./
#
GC                    0
AS                    0
DC                    0
#
MM                    1 
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 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.
#
# NP Parameters for nonpolar solvation energies if MS = 0
#
#   NPOPT - 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 = CAVITY_SURFTEN * SASA + CAVITY_OFFSET. 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 + CAVITY_SURFTEN * SASA + CAVITY_OFFSET.
#           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.
#   CAVITY_SURFTEN/CAVITY_OFFSET - Values used to compute the nonpolar
#           solvation free energy Gnp according NPOPT. The default values
#           are for NPOPT set to 0 and RADIOPT set to 0 (see above).
#           If NPOPT is set to 1 and RADIOPT set to 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:
#           CAVITY_SURFTEN: 0.04356
#           CAVITY_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 Gnp = SURFTEN * SASA + SURFOFF.
#
PROC                  2
REFE                  0
INDI                  1.0
EXDI                  80.0
SCALE                 2
LINIT                 1000
PRBRAD                1.4
ISTRNG                0.0
RADIOPT               0
NPOPT                 1
CAVITY_SURFTEN        0.0072
CAVITY_OFFSET         0.00
#
SURFTEN               0.0072
SURFOFF               0.00
#
################################################################################
@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
#
#################################################################################
@PROGRAMS
#
# Additional program executables can be defined here
#
#
################################################################################