#This is a correct input example
#Every line beginning with '#' is a comment
#Error occurs only for wrong keys
#case-sensitive
#------------------------------------------------

#Protein code and desired file type, possible values 'cif' or 'pdb'
#'cif' is for PDBx/mmCIF (default)
#'pdb' for standard PDB file (not implemented)

protein = 3clp
#3m5e
protein_filetype = pdb

#the model to take from the mmcif, if omitted model = 0 will be taken (starts from 0)
#Protein_model = 0
#the chain to choose from the xray structure (default A)
#Protein_chain = A

#The ph at which the hydrogens shall be added to the protein
#default = 7.0
ph = 7.0

#with which tool the pdb shall be fixed
#adding missing atoms, missing hydrogens and substituting
#non standard residues with standard ones
#default is pdbfixer (needs openmm and conda environment)

repairing_method = pdbfixer

#local tells if the program shall use a protein file that is already
#on the computer
#if 'no' (default) it will download it from the wwPDB database
#if 'yes' insert the absolute path in filepath
#any keyword different from yes and no will abort the program

local = yes
filepath = complex_ligand.pdb


#if ligand_in_protein = yes (default) ligand will be taken from the
#protein mmcif file

#if ligand_in_protein = no ligand will be given as input
#ligand = path/to/PDB
#the ligand shall be given as a pdb file (I suggest to use absolute path)

ligand_in_protein = yes
#ligand = ligand.pdb

#The program with which elaborate the ligand (optimization and potential)
#default primadorac (amber force field)

ligand_elaboration_program = primadorac
ligand_elaboration_program_path = ~/ORAC/trunk/tools/primadorac/primadorac.bash


#The molecular dynamics MD program
#of choice and the path to the executable

MD_program = gromacs
MD_program_path = gmx

#protein ff
#insert the name of the .ff dir without the .ff
#it is case sensitive
#if omitted default one is amber99sb-ildn
protein_tpg_file = amber99sb-ildn

#the solvent model that will be chosen
#standard is spce
# from the standard gromacs share directory
#other options can be none tip3p etc...
#check gromacs pdb2gmx -water documentation for more options
solvent_pdb = tip3p

#there can be custom residue substitutions for metal binding residues
#default standard
#standard, custom_zinc
residue_substitution = standard

#gromacs can use gpu accelerators
#there are 3 options
#auto (default)
#cpu uses only cpu even if gpus are available
#gpu forces to use gpus (using auto is HIGHLY RECOMENDED)
use_gpu = auto

#how many GPUs there are per node, default 1
#if gpus shall not be used it will be ignored
gpu_per_node = 4

#The kind of processor present on the HPC cluster
#default skylake
#other options broadwell knl (you can find them in the important_lists.py file)
kind_of_processor = skylake

# how many cores there are on the HPC cluster on each node
#default 64
number_of_cores_per_node = 64


########################################################
# ADVANCED OPTIONS, USE ONLY IF EXPERT
########################################################

#the box shape and dimentions for the protein ligand system (bound)
#box borders is the distance in nm between the protein and the box, default 1.2
box_borders = 1.2
#cubic and triclinic are the only 2 options, default cubic, the boxes will always have 90 angles
box_shape = cubic

#number of HREM replicas per each Battery for bound and unbound state, default 8
number_of_hrem_replicas_per_battery_bound = 24

number_of_hrem_replicas_per_battery_unbound = 8

#number of bound and unbound batteries per HREM, default auto
bound_batteries = 6
unbound_batteries = 4

#number of MD steps (reference state) for bound and unbound HREM and timesteps, dafault auto
n_steps_bound_hrem = 20000000
n_steps_unbound_hrem = 4000000
timestep_bound_hrem = 0.0015
timestep_unbound_hrem = 0.002

#kind of restraint in the bound and unbound HREM, default auto
#the sintax is the same of the gromacs mdp file: none, h-bonds, all-bonds
#auto will work most of the times
constraints_bound_hrem = h-bonds
constraints_unbound_hrem = h-bonds