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apr.in
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; APR input file
; AMBER settings
Amber16 = YES ; Use Amber 16 or older Amber versions (YES/NO)
hmr = YES ; Use hydrogen mass repartitioning (YES/NO); remember to use a relatively large stepsize (eq_dt and dt)
exe_path = 'pmemd.cuda' ; 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 = TIP3P ; currently support: TIP3P, TIP4P-Ew, OPC, SPC/E, CHCl3, MeOH, NMA
number_solvents = 2200
warning = NO ; 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 = :MOL ; Specify the residue name or the residue number of the ligand
H1 = :OCT@C11
H2 = :OCT@C23
H3 = :OCT@C51
G1 = :MOL@N1
G2 = :MOL@C6
; Variables for the NPT equilibration phase
eq_dt = 4 ; A step size of 4 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 = 4 ; A step size of 4 fs
nstlim = 625000 ; 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 = 2 ; 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 = YES ; 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]