• Check for close structural contacts and/or clashes in the model
  by entering the following commands:
  set complex [atomselect top "protein or resname TYL"] ; # Select atoms in the complex
  set clashes [measure contacts 1 $complex] ; # Find atoms within 1 Angstroms of each other
  foreach i [lindex $clashes 0] j [lindex $clashes 1] { ; # Report indices of clashing atoms
  puts "Atom $i clashes with atom $j" } ; # Indices can be used to visualize clashing atoms


• Note that no close contacts are identified for this system.


• Check forcispeptides by entering the following commands:
  package require cispeptide ; # Load cispeptide plugin
  cispeptide check -mol top ; # Run cis peptide check


• Note that twocispeptides are reported for this system, one that
  is known to be biologically important and one that contains
  proline and is likely not an artifact.

Step 8. Account for local salt ions.

• Run CIonize to place Naþand Cl– ions around the model by
  entering the following commands:
  package require cionize ; # Load cionize package
  namespace import ::cionize::*

  Run with a suffcient number of ions to saturate the model

  
  

  This example estimates 3x magnitude of system net charge

  
  

  set charge [expr {round([vecsum [[atomselect top "all"] get charge]])}] ; # System net charge
  set number [expr {abs($charge*3)}] ; # 3x magnitude of system net charge
  cionize -mol top -np 1 -mg -ions "{SOD $number 1} {CLA $number -1}"; # Run CIonize

  
  


• Load the PDB files generated by CIonize by entering the fol-
  lowing commands:
  mol new cionize-ions_1-SOD.pdb type pdb waitfor all ; # Load Na+ PDB
  mol new cionize-ions_1-CLA.pdb type pdb waitfor all ; # Load Cl- PDB


• Open theGraphical Representationswindow by clickingGra-
  phics!Representations...in theVMD Mainwindow.


• Create a clear representation of the ions in each PDB file by
  choosingVDWfrom theDrawing Methodmenu.


• Note that CIonize was run with enough ions to saturate the
  model, and unneeded ions were placed far away from it, along
  the edges of a box enclosure (Fig.8).


• Run psfgen to generate new PSF/PDB files that include local
  ions by entering the following commands:

258 Jodi A. Hadden and Juan R. Perilla