#
# Input parameters for mm_pbsa.pl
#
# Holger Gohlke
# 08.02.2002
#
################################################################################
@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 - Name of the parmtop file for the complex (not necessary for option GC).
#   RECPT - Name of the parmtop file for the receptor (not necessary for option GC).
#   LIGPT - Name of the 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 in single contributions (only works with MM and GB yet).
#
#   MM - Calculation of gasphase 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                test_traj
PATH                  ./
#
COMPLEX               1
RECEPTOR              0
LIGAND                0
#
COMPT                 ./mans.prmtop
RECPT                 
LIGPT                 
#
GC                    0
AS                    0
DC                    0
#
MM                    1 
GB                    1
PB                    0
MS                    0
#
NM                    0
#
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@GB
#
# GB parameters
#
#   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), 
#         Jayaram's et al. GB (3) or Jayaram's et al. MGB (4).
#   SALTCON - Concentration (in M) of 1-1 mobile counterions in solution.
#   EXTDIEL - Dielectricity constant for the surrounding solvent.
#
#   SURFTEN / SURFOFF - Values used to compute the nonpolar contribution Gnp to the 
#                       desolvation according to Gnp = SURFTEN * SASA + SURFOFF.
#
IGB                   4
SALTCON               0.00
EXTDIEL               80.0
#
SURFTEN               0.0072
SURFOFF               0.00
#
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