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 pluginRun 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 pluginRun 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