Step 7. Perform structural checks for the model.- Return to VMD’s command line and load the PSF/PDB files by
entering the following command:
mol new AAA_TYL_pH7.psf type psf waitfor all ;# Load PSF
mol addfile AAA_TYL_pH7.pdb type pdb waitfor all ; # Load PDB
package require psfgen ; # Load the psfgen plugin
topology toppar/top_all36_prot.rtf ; # Load CHARMM36
topology toppar/top_all36_cgenff.rtf ; # Load CGenFF
topology TYL.str ; # Load drug parameters
topology toppar/toppar_water_ions.str ; # Load TIP3P/ions
pdbalias residue P3M TIP3 ; # Interpret water as TIP3P
mol new TYL.mol2 type mol2 waitfor all ; # Load MOL2
set drug [atomselect top "resname TYL"] ; # Select drug molecule
$drug set segname TYL ; # Assign segname for psfgen
$drug writepdb TYL.pdb ; # Write segment PDB
mol new 4yji_pH7.pqr type pqr waitfor all ; # Load PQR
PROTEIN
set protein [atomselect top "protein"] ; # Select protein
$protein set segname AAA ; # Assign segname for psfgen
$protein writepdb AAA.pdb ; # Write segment PDB
segment AAA { ; # Build protein segment
pdb AAA.pdb ; # From segment PDB
first NTER ; # Patch with Zwitterionic N-terminus
last CTER } ; # Patch with Zwitterionic C-terminus
regenerate angles dihedrals ; # Critical after patching
coordpdb AAA.pdb ; # Assign coordinates from segment PDB
DRUG
segment TYL { ; # Build drug segment
pdb TYL.pdb } ; # From segment PDB
coordpdb TYL.pdb ; # Assign coordinates from segment PDB
CRYSTALLOGRAPHIC WATER
set water [atomselect top "resname P3M"] ; # Select water
$water set segname W0 ; # Assign segname for psfgen
$water writepdb W0.pdb ; # Write segment PDB
segment W0 { ; # Build water
pdb W0.pdb } ; # From segment PDB
coordpdb W0.pdb ; # Assign coordinates from segment PDB
writepsf AAA_TYL_pH7.psf ; # Output PSF
writepdb AAA_TYL_pH7.pdb ; # Output PDB
Molecular Dynamics Simulations of Protein-Drug Complexes 257