#
# Input parameters for mm_pbsa.pl
#
# Holger Gohlke
# 15.02.2012
#
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@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 to Ala during generation of snapshots from
#        trajectories.
#   DC - Decompose the free energies into individual contributions.
#        (When using DC, MM and GB must be set to 1, even if a PB decomposition
#         is also requested.)
#
#   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 the PB method and
#        computation 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 either
#        with the LCPO (GBSA == 1) or the ICOSA (GBSA == 2) method in sander 
#        (see below).
#        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               0
PARALLEL              0
#
PREFIX                at_g2
PATH                  snaps/
START                 1
STOP                  3000
OFFSET                50
#
COMPLEX               1
RECEPTOR              1
LIGAND                1
#
COMPT                 atg2.prmtop
RECPT                 at.prmtop
LIGPT                 g2.prmtop
#
GC                    0
AS                    0
DC                    0
#
MM                    0
GB                    0
PB                    0
MS                    0
#
NM                    1
#
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@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                  2
#
MAXCYC                10000
DRMS                  0.5
#
IGB                   0
SALTCON               0.00
EXTDIEL               80.0
SURFTEN               0.0072
#
DIELC                 4
#
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@PROGRAMS
#
# Additional program executables can be defined here
#
#
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