Computational Drug Discovery and Design

• Run minimization in NAMD on X processors by entering the
  following command:
  namd2 +pX min.conf >& min.log

# Input

structure AAA_TYL_pH7_ions_solvent_sc150mM.psf ; # Load PSF

coordinates AAA_TYL_pH7_ions_solvent_sc150mM.pdb ; # Load PDB

temperature 0 ; # Initial temperature

set bx 99.958 ; # Box dimensions (see Step 12)

set by 99.958

set bz 99.958

set cx 31.121 ; # Wrapping center (see Step 12)

set cy 1.777

set cz -2.136

# 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-off

pairlistdist 14.0 ; # Pairlist search radius

# Periodic Boundary Conditions

cellBasisVector1 $bx 0 0 ; # Box dimensions

cellBasisVector2 0 $by 0

cellBasisVector3 0 0 $bz

cellOrigin $cx $cy $cz ; # Wrapping center

wrapAll on ; # Wrap coordinates to wrapping center

PME yes ; # PME long-range electrostatics

PMEGridSpacing 1.0 ; # Grid spacing for PME

# Output

outputName min ; # Output file name prefix

binaryOutput yes ; # Output binary files

restartfreq 100 ; # Output frequencies

dcdfreq 100

xstFreq 100

outputEnergies 100

minimize 500 ; # Minimize 500 cycles

262 Jodi A. Hadden and Juan R. Perilla