Computational Biology(계산생물학)
Prof. Keun Woo Lee (이근우 교수)



ESP Calculations



  • Introduction

    • Calculating ESP (ElectroStatic Potential) means solving Poisson-Boltzmann equation. Currently we have two choices to achieve this: using Delphi or UHBD. DelPhi was developed/maintained by Honig group and UHBD (University of Houston Brownian Dynamics) was developed at University of Houston and managed by Briggs group. If you use Delphi module in InsightII, very powerful GUI will be provided. But, when you want to use UHBD, you will work in text mode and Grasp will be required to present the ESP map.

  • Theory

    • You can find some information about how to solve the Poisson-Boltzmann equation from documents: [ Delphi Manual : part, all ], [ Papers: (1, 2, 3 ).


A. ESP Calculations using DelPhi

  • System & InsightII Setup:

    • Prepare your PDB file in the working folder
    • Start InsightII (Type 'in2k' then enter)
    • Load the PDB file (In Main menu: Molecule/Get/PDB=on)
    • Add hydrogen atoms using Builder module:
      1) Module change to Builder
      2) In Builder menu: Modify/Hydrogens/Set_pH=on & Caping Mode=Charged
    • Assign the potential (use the CVFF potential):
      1) In the vertical menu bar: FF/Select/choose cvff.frc
      2) FF/Potential/Fix=on, Fix=on, Fix=on
    • Check that the partial charges you assigned:
      In Main menu: Molecule/Label/Label property=Partial Charge

  • DelPhi Setup:

    • Select the DelPhi module
    • In Delphi/Setup menu:

      • In Boundary menu:
        1) Full_Coulombic=on
      • In Grid menu:
        1) Display Grid=on
        2) Grid Center=Molecule_Region
        3) Solute Extent=50. (Ratio of your protein with the grid box. The 50 means 50% of the box.)
        4) Grid Resolution=Point Spacing
        5) Angstroms/GridPt = 0.5 . (This sets the spacing between grid points to 0.5 Angstroms. You can control this depending on your purpose.)
      • In Solute menu: (Keep the default values except for special cases.)
        1) Charge Option = Current_Charges
        2) Radius Option = VDW_radii
        3) Solute Dielectric = 2
        4) Charge Distribution = Point

      • In Solvent menu: (Keep the default values except for special cases.)
        1) Solvent Dielectric = 80.00 This forces the DelPhi calculation to automatically stop when there is no change in the potential between iterations
        2) Solvent Radius = 1.4 (For water. You can increase for large organic molecules.)
        3) Ionic Strength = 0.145 (mM)
        4) Ionic Radius = 2.00

      • In Iterations menu:
        Select Auto_Iterations (This forces the DelPhi calculation to automatically stop when there is no change in the potential between iterations.)

      • In Energies menu:
        Select Total_Plus_Grid (for Total ESP energy)

      • In Files menu:
        1) Select Potential_Map
        2) Potential Map Units = Potentials_kT/e
        3) Select Surface_Map

    • In Delphi/Run_DelPhi menu:
      • In Run menu:
        1) Execute Mode = background (Then, the DelPhi calculation will be running in the background so that you can use InsightII while the job is running.)
        2) Select Auto Get Grid . (Then, InsightII is able to automatically read the GRID potential (i.e. GRID file) when the job is done.)
        3) Click Excute to run and wait for the calculation to finish.

  • Analysis 1: Display Contours

    • In Delphi/Grid menu:
      • Select Get . (Load the grid file you created. Skip this step if you checked Auto Get Grid previously.)
      • Select Contour :
        1) For Grid Name select the grid file created
        2) For Contour Name Root type anything (ex. "esp1" ).
        3) For Contour Level type -1.0
        4) For Display Stype choose Lines
        5) For Color choose red
        InsightII will display red contours for all the points on the grid with a potential value equal to -1.0 kcal/mol/e
        6) Repeat above for a Contour Level equal to 1.0 and colour those contours Blue

  • Analysis 2: Display Planes

    • In Delphi/Grid menu:
      • Select Get . (Skip this if you already load the grid file in the previous step.)
      • Select Slice :
        1) For Grid Name select the grid file created
        2) For Spectrum Name select DELPHI_SPECTRUM
        3) Execute (Then, a white plane will appear through the molecule.)
        4) Move the position of the plane by sliding the slider under Parameters

    [ Result Images ]


     

    B. ESP Calculations using UHBD



과 목: 계산생물학/생물정보학 (경상대학교 생화학과)
담당교수: 이근우 (kwlee@gnu.ac.kr)


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