3 Electrostatics potential maps and field lines in VMD

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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