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Calculation Setup

Visualization of Electrostatic Potentials

 Solvation Energy Calculation


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It is often desirable to calculate lower-resolution electrostatic potentials suitable for interactive display and manipulation. The potential surrounding a molecule can be indicative of electrostatic complimentarity between two binding partners or of electrostatic steering that may influence surrounding diffusional processes. We will use a small small protein-ligand system FK506 binding protein (FKBP12) and the ligand 4-hydroxy-2-butanone.

We can generate one input script for multiple molecules as is shown below. The major elements of this calculation are:

  1. Read in the molecular data.
  2. Calculate the electrostatic potential.
  3. Write out the molecular surface (vdw surface in this case) and the potential.

Example Input File - FKBP12 - 4-hydroxy-2-butanone 

          

read 
    mol pqr lig.pqr       # Read ligand (mol 1)
    mol pqr prot.pqr      # Read protein (mol 2)
end

elec name lig
    mg-manual             # Use the multigrid method
    dime 33 65 33         # Grid dimensions
    nlev 4                # Multigrid levels
    glen  6 15 8          # Grid length
    gcent mol 1           # Center on complex
    mol 1                 # Solute molecule             
    lpbe                  # linearized PBE             
    bcfl sdh              # Monopole boundary conditions
    ion 1 0.000 2.0       # Zero ionic strength
    ion -1 0.000 2.0                   
    pdie 2.0              # Solute dielectric
    sdie 78.00            # Solvent dielectric
    chgm spl2             # Charge disc method (spline)
    srfm mol              # Smoothed molecular surface
    srad 1.4              # Solvent radius
    swin 0.3              # Surface cubic spline window
    temp 298.15           # Temperature
    gamma 0.105           # Surface tension (in kJ/mol/A^2)
    calcenergy no
    calcforce no
    write pot dx lig_pot   # Write potential to lig_pot.dx
    write vdw dx lig_vdw   # Write vdw surface to lig_vdw.dx
end

elec name prot            # SAME AS ABOVE FOR PROTEIN
    mg-manual                          
    dime 65 33 33
    nlev 4                             
    glen 82.465  58.876  58.446 
    gcent mol 2
    mol 2
    lpbe
    bcfl sdh
    ion 1 0.000 2.0
    ion -1 0.000 2.0
    pdie 2.0
    sdie 78.00
    chgm spl2
    srfm smol
    srad 1.4
    swin 0.3
    temp 298.15
    gamma 0.105
    calcenergy no
    calcforce no
    write pot dx prot_pot            
    write vdw dx prot_vdw
end
quit

Execute this script with the following:

        

apbs fkbp_vis.in > fkbp_vis.out

After execution you should have the following files:

Visualization with VMD

We will use VMD to render the potential onto the molecular surfaces and to create some isosurfaces. The following script can be run automatically or each command can be manually executed within VMD (see comments in bold). The latter will be more instructive.

To run the script automatically open VMD 1.8.3a15. Open the Tk Console under Extensions. Change to the visualization directory and play the vmd script with %play fkbp_vis.vmd 

          
          
  # Load protein and ligand
  #  [File -> New Molecule]
  mol load pqr prot.pqr                      #id 0
  mol load pqr lig.pqr                       #id 1

  # Render the protein as Ribbons 
  #  [Graphics -> Representations -> Drawing Methods => NewRibbons, Coloring Method => ColorID 4]
  mol modstyle 0 0 NewRibbons
  mol modcolor 0 0 ColorID 4

  # Render the ligand 
  #  [Graphics -> Representations -> Drawing Methods => CPK, Coloring Method => ColorID 8]
  mol modstyle 0 1 CPK
  mol modcolor 0 1 ColorID 8

  # Load vdw surface and potential 
  #  [File -> New Molecule -> lig_vdw.dx and lig_pot.dx on same molecule!]
  mol load dx lig_vdw.dx                     #id 2
  mol addfile lig_pot.dx type dx molid 2

  # Change Representation Method to Solid Surface 
  #  [Graphics -> Representations ->Representation Method => Solid Surface] 
  # Change Display to Isosurface
  #  [Graphics -> Representations ->Display => Isosurface] 
  mol modstyle 0 2 Isosurface 0.5 0.0 0.0 0.0
  # Change Surface coloring to Volume on the potential(id2)
  #  [Coloring Method => Volume, selection 1]
  mol modcolor 0 2 Volume 1
  # Change Surface from opaque to transparent
  #  [Material => Transparent]
  mol modmaterial 0 2 Transparent

  # Change color scale to RWB
  #  [Graphics -> Colors -> ColorScale -> Method => RWB]
  color scale method RWB
  mol scaleminmax 2 0 -5.0 5.0

  #Load vdw surface and potential
  #  [File -> New Molecule ... again prot_pot.dx on same molecule]
  mol load dx prot_vdw.dx          				#id 3
  mol addfile prot_pot.dx type dx molid 3

  #Add blue isosurface at +1.0
  #  [Graphics -> Representations ->Representation Method => Solid Surface] 
  #  [Display => Isosurface, Isovalue => 1.0, Coloring Method => ColorID 0] 
  mol modstyle 0 3 Isosurface 1.0 1.0 0.0 0.0 1
  mol modcolor 0 3 ColorID 0
  mol modmaterial 0 3 Transparent

  #Add red isosurface at -1.0
  #  [Graphics -> Representations -> Create Rep]
  #  [Representation Method => Solid Surface, Display => Isosurface, Isovalue => 1.0, Coloring Method => ColorID 0]]
  mol representation Isosurface -1.0 1.0 0.0 0.0 1
  mol color ColorID 1
  mol selection all
  mol material Transparent
  mol addrep 3
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Calculation Setup Solvation Energy Calculation