Computational Drug Discovery and Design

# Input

structure AAA_TYL_pH7_ions_solvent_sc150mM.psf ; # Load PSF

coordinates AAA_TYL_pH7_ions_solvent_sc150mM.pdb ; # Load PDB

set restraints restraints.pdb ; # Load restraints PDB

set temperature 50 ; # Initial temperature

temperature $temperature

binCoordinates min.restart.coor; # Restart information

extendedSystem min.restart.xsc

# Force Field Information

paraTypeCharmm on ; # Use CHARMM

parameters toppar/par_all36_prot.prm ; # Load CHARMM36

parameters toppar/par_all36_carb.prm

parameters toppar/par_all36_lipid.prm

parameters toppar/par_all36_cgenff.prm ; # Load CGenFF

parameters toppar/toppar_water_ions.str ; # Load TIP3P/ions

parameters TYL.str ; # Load drug parameters

exclude scaled1-4 ; # Exclude 1-2s and 1-3s, scale 1-4s

1-4scaling 1.0 ; # 1-4 scaling factor

cutoff 12.0 ; # Cut-off radius for non-bonded interactions

switching on ; # Scale smoothly to zero

switchdist 10.0 ; # Scale smoothly from here to cut

pairlistdist 14.0 ; # Pairlist search radius

# Periodic Boundary Conditions

wrapAll on ; # Wrap coordinates

PME yes ; # PME long-range electrostatics

PMEGridSpacing 1.0 ; # Grid spacing for PME

margin 1.5 ; # For box equilibration

# Integrator Parameters

timestep 2.0 ; # Time step

rigidBonds all ; # Constrain bonds to hydrogen

useSettle on ; # Use SETTLE for water molecules

nonbondedFreq 1 ; # Frequency to recalculate nonbonded interactions

fullElectFrequency 2 ; # Frequency to recalculate fullelectrostatics

longSplitting c2 ; # Long/short range splitting method

stepspercycle 20 ; # Pairlist update

# Constant Temperature Control

langevin on ; # Langevin thermostat

langevinTemp $temperature ; # Target temperature

langevinDamping 1.0

langevinHydrogen off

264 Jodi A. Hadden and Juan R. Perilla