Computational Drug Discovery and Design

resetpsf ; # Reset psfgen

readpsf AAA_TYL_pH7.psf ; # Read PSF

coordpdb AAA_TYL_pH7.pdb ; # Read PDB

segment SOD { ; # Build Na+ segment

pdb cionize-ions_1-SOD.pdb } ; # From Cionize PDB

coordpdb cionize-ions_1-SOD.pdb ; # Assign coordinates from PDB

segment CLA { ; # Build Cl- segment

pdb cionize-ions_1-CLA.pdb } ; # From Cionize PDB

coordpdb cionize-ions_1-CLA.pdb ; # Assign coordinates from PDB

writepsf AAA_TYL_pH7_cionize.psf ; # Output PSF

writepdb AAA_TYL_pH7_cionize.pdb ; # Output PDB

mol new AAA_TYL_pH7_cionize.psf type psf waitfor all; # Load PSF

mol addfile AAA_TYL_pH7_cionize.pdb type pdb waitfor all ; # Load PDB

# Delete ions not within 20 Angstroms of the model based on indices

set bad [atomselect top "(all not within 20 of protein)"]

foreach segid [$bad get segid] resid [$bad get resid] {

delatom $segid $resid }

writepsf AAA_TYL_pH7_ions.psf ; # Output PSF

writepdb AAA_TYL_pH7_ions.pdb ; # Output PDB

Fig. 8CIonize places ions around the model according to local electrostatic potential; unneeded ions are
placed far away from the model

Molecular Dynamics Simulations of Protein-Drug Complexes 259