#
# Input parameters for mm_pbsa.pl
# This example just generates snapshots from a trajectory file
#
# 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                md35                      
PATH                  ./
#
COMPLEX               1
RECEPTOR              1
LIGAND                1
#
COMPT                 ../../prmtop/cpt_wild_complex3.prmtop
RECPT                 ../prmtop/cpt_wild_receptor3.prmtop
LIGPT                 ../prmtop/cpt_ligand.prmtop
#
GC                    1
AS                    0
DC                    0
#
MM                    0 
GB                    0
PB                    0
MS                    0
#
NM                    0
#
################################################################################
@MAKECRD
#
# The following parameters are passed to make_crd_hg, which extracts snapshots
#   from trajectory files. (This section is only relevant if GC = 1 OR AS = 1 above.)
#
#   BOX - "YES" means that periodic boundary conditions were used during MD 
#         simulation and that box information has been printed in the
#         trajecotry files; "NO" means opposite.
#   NTOTAL - Total number of atoms per snapshot printed in the trajectory file
#            (including water, ions, ...).
#   NSTART - Start structure extraction from NSTART snapshot.
#   NSTOP - Stop structure extraction at NSTOP snapshot.
#   NFREQ - Every NFREQ structure will be extracted from the trajectory.
#
#   NUMBER_LIG_GROUPS - Number of subsequent LSTART/LSTOP combinations to
#                       extract atoms belonging to the ligand.
#   LSTART - Number of first ligand atom in the trajectory entry.
#   LSTOP - Number of last ligand atom in the trajectory entry.      
#   NUMBER_REC_GROUPS - Number of subsequent RSTART/RSTOP combinations to
#                       extract atoms belonging to the receptor.
#   RSTART - Number of first receptor atom in the trajectory entry.
#   RSTOP - Number of last receptor atom in the trajectory entry.      
#   Note: If only one molecular species is extracted, use only the receptor
#         parameters (NUMBER_REC_GROUPS, RSTART, RSTOP).
#   
BOX                   YES
NTOTAL                94336
NSTART                1
NSTOP                 100   
NFREQ                 10 
#
NUMBER_LIG_GROUPS     1
LSTART                10862
LSTOP                 10903
NUMBER_REC_GROUPS     1
RSTART                1
RSTOP                 10861
#
#################################################################################
@TRAJECTORY
#
# Trajectory names
#
#   The following trajectories are used to extract snapshots with "make_crd_hg":
#   Each trajectory name must be preceeded by the TRAJECTORY card.
#   Subsequent trajectories are considered together; trajectories may be 
#     in ascii as well as in .gz format. 
#   To be able to identify the title line, it must be identical in all files. 
#
TRAJECTORY            ../md35.mdcrd.gz
#
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@PROGRAMS
#
# Program executables
#
DELPHI                /home/gohlke/src/delphi.98/exe.R10000/delphi
#
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