Step 9. Establish the system box.

• Determine the dimensions of an appropriate cubic box to
  enclose the model by entering the following commands:
  mol new AAA_TYL_pH7_ions.psf type psf waitfor all ; # Load PSF
  mol new AAA_TYL_pH7_ions.pdb type pdb waitfor all ; # Load PDB
  set model [atomselect top "all"] ; # Select model

set center [measure center $model] ; # Measure model center, dimensions, and longest box vector

set dimens [vecsub [lindex [measure minmax $model] 1] [lindex [measure minmax $model] 0]]

set maxvec [expr {max([lindex $dimens 0],[lindex $dimens 1],[lindex $dimens 2])}]

set boxpad 15 ; # At least 15 Angstroms between model and box edge recommended

set boxlen [expr ($maxvec + 2*$boxpad)/2] ; # Length of cubic box vector

set minx [expr [lindex $center 0] - $boxlen] ; # Box min

set miny [expr [lindex $center 1] - $boxlen]

set minz [expr [lindex $center 2] - $boxlen]

set boxmin [list $minx $miny $minz]

set maxx [expr [lindex $center 0] + $boxlen] ; # Box max

set maxy [expr [lindex $center 1] + $boxlen]

set maxz [expr [lindex $center 2] + $boxlen]

set boxmax [list $maxx $maxy $maxz]

Step 10. Immerse the model in solvent.

• Generate a cubic water box with the dimensions determined
  above by entering the following commands:
  package require solvate ; # Load the solvate plugin

  Run solvate with command as a single line:

  
  

  solvate AAA_TYL_pH7_ions.psf AAA_TYL_pH7_ions.pdb -minmax [list $boxmin $boxmax] -o
  AAA_TYL_pH7_ions_solvent -s W

  
  

Step 11. Account for salt concentration.

• Neutralize the system and add salt concentration of 150 mM by
  entering the following commands:
  package require autoionize ; # Load the autoionize plugin

  Run autoionize with command as a single line:

  
  

  autoionize -psf AAA_TYL_pH7_ions_solvent.psf -pdb AAA_TYL_pH7_ions_solvent.pdb -cation SOD -
  anion CLA -sc 0.150 -o AAA_TYL_pH7_ions_solvent_sc150mM -seg I1

  
  


• Load the PSF/PDB files for the final model for visualization by
  entering the following commands:
  mol new AAA_TYL_pH7_ions_solvent_sc150mM.psf type psf waitfor all ; # Load PSF
  mol addfile AAA_TYL_pH7_ions_solvent_sc150mM.pdb type pdb waitfor all ; # Load PDB


• The setup phase of the project is now complete. The final model
  of the protein–drug complex at pH 7, including crystallographic

260 Jodi A. Hadden and Juan R. Perilla