#
# Input parameters for mm_pbsa.pl
#   This example does decomposition by pairwise residues
#
# 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).
#   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                ubi
PATH                  ./
#
COMPLEX               1
RECEPTOR              0
LIGAND                0
#
COMPT                 1ubq.prm.top
RECPT                 XXX
LIGPT                 XXX
#
GC                    0
AS                    0
DC                    1
#
MM                    1 
GB                    1
PB                    0
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 LCPO 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                4
#
COMREC                1-76
COMLIG                0-0
COMPRI                1-76
RECRES                1-76
RECPRI                1-76
RECMAP                1-76
LIGRES                0-0
LIGPRI                0-0
LIGMAP                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                 1.0
#
################################################################################
@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                  2
SALTCON               0.00
EXTDIEL               80.0
INTDIEL               1.0
#
SURFTEN               0.0072
SURFOFF               0.00
#
################################################################################
@PROGRAMS
#
# Program executables
#
DELPHI                /home/gohlke/src/delphi.98/exe/delphi
#
################################################################################