@GENERAL
PREFIX                qq2
PATH                  ./snapshots
#
COMPLEX               1
RECEPTOR              1
LIGAND                1
#
COMPT                 ./qq2.prmtop
RECPT                 ./jmjd.prmtop
LIGPT                 ./tail.prmtop 
#
GC                    0
AS                    0
DC                    0
#
MM                    1 
GB                    1
PB                    1
MS                    0
#
NM                    0
#
################################################################################
@PB
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
#
#
################################################################################