; APR input file

; AMBER settings
Amber16  = NO              ; Use Amber 16 or older Amber versions (YES/NO)
hmr =  NO                  ; Use hydrogen mass repartitioning (YES/NO); remember to use a relatively large stepsize (eq_dt and dt)
exe_path = '$PMEMD_RUN'    ; Other avaiable options include: 'mpirun -np 12 pmemd.MPI', 'pmemd', 'sander'... 
temperature  = 298.15      ; For MD simulations and TI analysis (in Kelvin) 
perturb = NO               ; Perturb GAFF parameters (YES/NO); new_parameters.dat needs to be provided in setup/param_files

; Variables for setting up umbrella sampling windows          
attach_list = [0.00, 0.40, 0.80, 1.60, 2.40, 4.00, 5.50, 8.65, 11.80, 18.10, 24.40, 37.00, 49.60, 74.80]
translate_list  = [0.00, 0.40, 0.80, 1.20, 1.60, 2.00, 2.40, 2.80, 3.20, 3.60, 4.00, 4.40, 4.80,
               5.20, 5.60, 6.00, 6.40, 6.80, 7.20, 7.60, 8.00, 8.40, 8.80, 9.20, 9.60, 10.00,
               10.40, 10.80, 11.20, 11.60, 12.00, 12.40, 12.80, 13.20, 13.60, 14.00, 14.40,
               14.80, 15.20, 15.60, 16.00, 16.40, 16.80, 17.20, 17.60, 18.00]

; Force constants for restraints
distance_force  = 5.0    ; kcal/mol/Angstrom**2
angle_force     = 100.0  ; kcal/mol/rad**2

; Solvation
solvent_model     = CHCl3    ; currently support: TIP3P, TIP4P-Ew, OPC, SPC/E, CHCl3, MeOH, NMA  
number_solvents   = 376
warning           = YES      ; A warning message can be printed out if the number of water molecules requested above is not close to estimation (YES/NO)

; Counterions 
neutralizing_cation = Na+ ; for neutralization only, not used for positively charged or neutral system
neutralizing_anion  = Cl- ; for neutralization only, not used for negatively charged or neutral system

cations         =  Na+    ; Atom type if extra salt is needed to mimic buffer conditions
number_cations  =  0      ; 
anions          =  Cl-    ; Atom type if extra salt is needed to mimic buffer conditions
number_anions   =  0      ; 

; Specifying receptor and ligand atoms for setting up restraints
lIG        = :PIR         ; Specify the residue name or the residue number of the ligand
H1         = :CB6@C8 
H2         = :CB6@C2
H3         = :CB6@C10
G1         = :PIR@N1
G2         = :PIR@C4

; Variables for the NPT equilibration phase
eq_dt          = 2       ; A step size of 2 fs 
eq_nstlim      = 1250    ; Run 1250 equilibraton steps, to give a equilibration time of 5 ps per cycle and 250 ps in total (the number of iterations is fixed as 50)
eq_barostat    = 2       ; Options for barostat; 1 is Berendsen and 2 is Monte Carlo
eq_cutoff      = 9       ; 9 Angstrom cutoff distance for the van der Waals interactions

; Variables for production runs 
dt             = 2       ; A step size of 2 fs 
nstlim         = 2500000 ; Run 1,250,000 molecular dynamics steps, to give a simulation time of 2.5 ns per cycle 
ntpr           = 250     ; Write to the output file every 250 steps (1 ps) 
ntwx           = 250     ; Write to the trajectory file every 250 steps (1 ps) 
barostat       = 1       ; Options for barostat; 1 is Berendsen and 2 is Monte Carlo 
cutoff         = 9       ; 9 Angstrom cutoff distance for the van der Waals interactions
strip_solvent_ions = NO  ; Strip water and ions in the MD trajectories (YES/NO), YES is recommended to save disk space

maxcycle       =  20     ; the number of trajectories in one window. The maximum number is fixed as 20.
maxsem_attach  = 0.02    ; the threshold of standard error of the mean (SEM) for the forces in the attach phase; in kcal/mol
maxsem_pull    = 0.1     ; the threshold of SEM for the forces in the pulling phase; in kcal/mol
maxsem_release = 0.02    ; the threshold of SEM for the forces in the release phase, only used if there are (additional) conformational restraints; The value should match sem_attach

jacks        = NO        ; Use conformational restraints (YES/NO)

; Used if there are conformational restraints (jacks = YES)
jacks_distance = 15.0     ; Angstrom, value may vary with systems        
jacks_force = 25.0        ; kcal/mol/Angstrom**2, values may vary with systems

jacks_list =  [:OCT@O20,   :OCT@O19,
              :OCT@O13,   :OCT@O18,
              :OCT@O14,   :OCT@O17,
              :OCT@O15,   :OCT@O16,
              :OCT@C61,   :OCT@C50,
              :OCT@C62,   :OCT@C49,
              :OCT@C56,   :OCT@C67,
              :OCT@C55,   :OCT@C68,
              :OCT@C79,   :OCT@C85,
              :OCT@C75,   :OCT@C81,
              :OCT@C69,   :OCT@C91,
              :OCT@C74,   :OCT@C96]