# **********************************************************
# *                                                        *
# *              R E F I N E . P A R S                     *
# *                                                        *
# **********************************************************
# This parameter file contains all necessary information for a refinement
# in explicit solvent using xplor

# NOTES FOR USAGE:
# change pathnames as appropriate for user and project name
# use absolute pathnames for the directories amd leave out trailing slashes


# Directory where the project is run: 
PROJECTDIR   = /u/lytle/at5g39720/9valid/58g

# Location of input coordinate, psf, constraint files:
INPUTDIR    = /u/lytle/at5g39720/9valid/58g/input 

# ----- YOU SHOULDN'T HAVE TO CHANGE ANYTHING BELOW THIS LINE -----

#########################
# FILES AND DIRECTORIES:#
#########################

# Set a temporary directory (default='/tmp'):
# This is needed since some programs cannot deal with long pathnames
# These programs are run in the TMPDIR when necessary
# use names up to 20 chars for the TMPDIR
TMPDIR       = /tmp

# Location of python scripts:
SCRIPTSDIR   = /u/francis/waterrefine/scripts

# Total number of inputstructures:
NINPUTSTRUCTURES  = 20 

# Base filename for input structures (pdb_base_xxx.pdb):
PDB_BASE     = 1xxx

# Filename of the XPLOR psf file:
PSF_FILE     = 1xxx.psf

# Filename of the XPLOR NOE table:
NOE_FILE     = 1xxx_noe.tbl

# Filename of the XPLOR CDIH table:
CDIH_FILE    = 1xxx_dihe.tbl

# Filename of the XPLOR COUP restraints table:
COUP_FILE    = 

# Filename of the XPLOR SANI restraints table:
SANI_FILE    = 

# Filename of the XPLOR VEAN restraints table:
VEAN_FILE    = 

#########################
# REFINEMENT PARAMETERS:#
#########################

# Type of averaging used for the NOE restraints:
NOE_AVE      = sum

# NOE restraints acceptance criterium (Angstrom):
NOE_ACCEPT   = 0.5

# Dihedral angle restraints acceptance criterium (degrees):
CDIH_ACCEPT  = 5.0

# COUP restraints acceptance criterium:
COUP_ACCEPT  = 1.0

# SANI restraints acceptance criterium:
SANI_ACCEPT  = 0.0

# VEAN restraints acceptance criterium:
VEAN_ACCEPT  = 5.0

# Number of steps for the heating stage:
# TIME FOR HEATING STAGE: 0.015*HEAT_STEPS ps
# 5 CYCLES, TIMESTEP 0.003 ps
# Normally HEAT_STEPS = 200
HEAT_STEPS   = 200
#HEAT_STEPS   = 10

# Number of steps for the hot stage:
# TIME FOR HEATING STAGE: 0.004*HOT_STEPS ps
# 1 CYCLE, TIMESTEP 0.004 ps
# Normally HOT_STEPS = 2000
HOT_STEPS    = 2000
#HOT_STEPS    = 10

# Number of steps for the cool stage:
# TIME FOR HEATING STAGE: 0.080*HEAT_STEPS ps
# 20 CYCLES, TIMESTEP 0.004 ps
# Normally COOL_STEPS = 200
COOL_STEPS   = 200
#COOL_STEPS   = 10

# Random seed number used for velocity generation in XPLOR:
SEED         = 12396

# Zonefile for RMSD calculations:
ZONEFILE     = zone_file_with_no_zone

# Atom selection for RMSD calculations (All= separate calculations of Heavy, CA and backbone RMSD)
# Options: All, Heavy, Ca and BB
SELECTION    = All

# Type of Energy Sorting of pdb files:
# Options: restraint_energy, noe_energy, overall_energy
ENERGYSORT   = restraint_energy


###################
# FURTHER OPTIONS:#
###################

# Run the resampling procedure on a cluster (y/n):
RUN_CLUSTER  = y

# Que command for run on a cluster:
#QUEU_CLUSTER = /usr/local/pbs/bin/qsub -l nodes=1:ppn=1
# JFD defines: input output is organised in script.

QUEU_CLUSTER = qsub -q seriallong -o ~/job_io -e ~/job_io -l nodes=1:ppn=1 -S /bin/tcsh -V