3.1 Install APBS at Ubuntu 18.04

• sudo apt-get update -y
• sudo apt-get install -y apbs

Note: -y flag means to assume yes and silently install, without asking you questions in most cases.

3.2 Make potential surface map

• load pdb
• build structure: extenstions > modeling > automatic PSF builder
• minimize structure using NAMD
• load minimized strcture: i.e. mol load psf test.psf pdb min.coor
• do apbs calculation: Extensions > Analysis > APBS Electrostatics > Edit > Setting > Working Directory > APBS location > use charmm radii > OK > select 0 line > Edit > Run
• look at the log file to find output location, move pot.dx to working directory
• load pot.dx into the same mol: mol addfile pot.dx
• Drawing > surf
• Coloring > Volume
• Trajectory > set color scale range -10 to 10

3.2 Make potential field lines

• Drawing > Fieldlines
• Adjust settings for optimal visualization
  • Size: 2
  • GradientMag: 8.3
  • Min Length: 1.00
  • Max Length: 200.00
• Coloring > Volume
• Trajectory > Set Color Scale from -0.5 to 0.5
• Create new Rep
  • Coloring > Name
  • Drawing > NewCartoon