Generating and Displaying an Electostatic Surface

From Bridges Lab Protocols
Revision as of 00:38, 10 October 2009 by Davebridges (Talk | contribs) (→‎Generate PQR File for the Structure)

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Programs Required

  • Pymol
  • APBS

Generate PQR File for the Structure

  1. Download or generate PDB file.
  2. Go to the PDB2PQR server at http://pdb2pqr-1.wustl.edu/pdb2pqr/. The default settings (AMBER forcefield, internal naming scheme), are ok. Check off the prepare APBS input file
  3. Save the pqr file and the APBS input file.
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