Generating and Displaying an Electostatic Surface: Difference between revisions
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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) are ok. Check off the | #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 Create an 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. | ||