Generating and Displaying an Electostatic Surface: Difference between revisions
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#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 | #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 | ||
#Save the pqr file and the APBS input file. | #Save the pqr file and the APBS input file. | ||
[[Category: Structures]] | |||
[[Category: PyMol]] | |||
[[Category: Bioinformatics]] | |||
Revision as of 00:39, 10 October 2009
Programs Required
- Pymol
- APBS
Generate PQR File for the Structure
- Download or generate PDB file.
- 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
- Save the pqr file and the APBS input file.