Analysis of Your Favorite Protein
Dealing with Problematic PDB Files
Practice creating the electrostatic potential surface with a protein of your choice. There is a good chance that it will not work the first time. Some common issues are:
- The structure contains ligands unkown to APBS. In general, these can be safely deleted unless the field created by the ligand is thought to be important.
- The structure contains alternative conformations of amino acids. This is becoming more common as more high-resolution structures are being generated. You need to delete the alternative chains and rename amino acids to appropriate three-letter codes.
- The C-terminus is not correctly recognized by the program. Different versions of the APBS plugin may handle this situation differently. Sometimes deleting the N-terminal residue (remove atoms in PyMOL) might solve the problem.
- Too many residues have missing atoms and manual mutagenesis becomes impractical. Reduce all such residues to alanines using a the DockPrep function in UCSF chimera.
- There are many copies of the proteins in the published structure file and this confuses APBS or puts too large of a demands on the computational resources. Work with one copy of the protein molecule.
The PDB2PQR Server
The issues described above are being addressed in the developers of the PDB2PQR conversion program. The PQR file is a modified PDB file in which every atom has additional columns defining the charge and radius of the atom. The PQR file is the input format for APBS. One can now use the PDB2PQR web server to generate PQR files for proteins in the RCSB Protein Databank or for structures stored on the local server. To use these PQR files, save them on the hard drive and select Use another PQR under the Main tab in the APBS Tools plugin. Then enter the path for the PQR file in the field below and run APBS.
Thank you and good luck with PyMOL
Kalju