PyMol & Multiwfn Electrostatic Potential (ESP) Visualization

Generate ESP .cub file from the Multiwfn and plot it in PyMol

Related Multiwfn Documents
http://sobereva.com/443
http://sobereva.com/196

Related PyMol Documents
https://pymolwiki.org/index.php/Ramp_New

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Generate .fchk file with Gaussian

• Run a single point calculation and save the wavefuncation information to the .chk file %chk=xxx.chk
• Make the formchk file and refine it with sed. (Make it readable to GaussView)

  for i in *.chk; do formchk $i ${i%chk}fchk && sed -i 's/MM charges/MM charge /g' ${i%chk}fchk && sed -i 's/MicOpt/Opt   /g' ${i%chk}fchk; done

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Generate .cub file with Multiwfn

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Single file

• set the cubegen path in $Multiwfn_HOME/setting.ini
  This greatly accelerate the calculation
• open Multiwfn.exe
• load the .fchk file
• Run ESP calculation
  The following numbers are the Multiwfn control-index

  5     # Output and plot specific property within a spatial region (calc. grid data)
  1     # Electron density  
  2     # Medium quality grid, covering whole system
  2     # Export data to Gaussian-type cube file in current folder

  Here we got the .cub file for ESP isosurface density.cub

  0     # Return to main menu
  5     # Output and plot specific property within a spatial region (calc. grid data)
  12    # Total electrostatic potential (ESP)
  1     # Low quality grid   , covering whole system 
        # Running: "cubegen 4 potential=SCF xxx.fchk ESPresult.cub -1 h ESPgridtmp.cub > nouseout"
  2     # Export data to Gaussian-type cube file in current folder

  Here we got the .cub file for ESP color mapping totesp.cub

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Multiple file

A .bat/.ps1 file can help dealing with multiple .fchk

Multiwfn XXX.fchk < ESPiso.txt
move /Y density.cub density1.cub
move /Y totesp.cub ESP1.cub

The .txt file contain the control-index listed above

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Visualize the surface with PyMol

• open the structure (save a .mol2 from any of the .cub) and these two .cub files
• Use “Other Visualization Settings for structures” from https://www.shaoqz.cn/2020/06/29/PyMol-Orbital/
• Build Isosurface

  isosurface ESP1, density, 0.002
  set transparency, 0.2

  Grammer: isosurface {new object name}, {.cub name}, {isovalue}
• Color the surface with ESP

  ramp_new ramp1, totesp, [0, 0.3, 0.36], [blue, white, red]
  color ramp1, ESP1

  Grammer: ramp_new {new object name}, {ESP .cub name}, [Value list], [Corresponding color list]
  Grammer: color {color object}, {object}

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The extreme point analysis

In Multiwfn with the .fchk loaded

12          # Quantitative analysis of molecular surface
3           # Spacing of grid points for generating molecular surface:  0.250000
0.15
0           # Start analysis now!
5           # Export molecule as pdb format file (optional)
name.pdb    
6           # Export all surface vertices to vtx.pdb in current folder (optional)
2           # Export surface extrema as pdb file

Maxima is presented as carbon
Minima is presented as oxygen