Difference between revisions of "Generating and Displaying an Electostatic Surface"
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===Generate PQR and PX Files for the Structure=== | ===Generate PQR and PX Files for the Structure=== | ||
#Download or generate PDB file. | #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) | + | #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 button. |
#Save the pqr file and the APBS input file. | #Save the pqr file and the APBS input file. | ||
#Run APBS as '''apbs inputfile.in'''. This will generate a *.dx file. | #Run APBS as '''apbs inputfile.in'''. This will generate a *.dx file. | ||
Revision as of 00:52, 10 October 2009
Programs Required
Generate PQR and PX Files 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 button.
- Save the pqr file and the APBS input file.
- Run APBS as apbs inputfile.in. This will generate a *.dx file.
Visualizing Electrostatic Surface
- Open pdb file then dx file in pymol.
- Go to plugin -> apbs tools -> visualization.
- Go to the visualization tab.
- Click on show and adjust settings to -10kV to 10kV and press show again.
