Computational Drug Discovery and Design

• Inspect the parameters in TYL.str, and note that their penalty
  scores are insignificant.

Step 5. Account for pH of the model.

• Visit the PDB2PQR server (http://nbcr-222.ucsd.edu/
  pdb2pqr_2.1.1) and choose the option toupload a PDB file,
  selecting 4yji.pdb from your working directory (Fig.7).


• Choose CHARMM for theforcefieldandoutput naming scheme
  options.


• Also select options toEnsure that new atoms are not rebuilt too
  close to existing atoms and Optimize the hydrogen bonding
  network.


• UnderpKa options, enter pH 7 and choose the option toUse
  PROPKA to assign protonation states at the provided pH.


• Click theSubmitbutton to continue.


• Once the status of the PDB2PQR job updates to complete,
  download the 4yji.pqr file and save it to your working directory
  as 4yji_pH7.pqr.

Step 6. Generate PSF/PDB files for the model.

• Return to VMD’s command line and run psfgen to generate
  PSF/PDB files for the model by entering the following
  commands:

Fig. 6Maestro is recommended for generating a correctly formatted MOL2 file

Molecular Dynamics Simulations of Protein-Drug Complexes 255