I've been trying to generate an electrostatic potential map of the surface of a protein using Pymol but haven't been successful. I'm working with the latest version of pymol (0.98, windows version), which brings the APBS plugin (I have as well installed the APBS plugin "apbs_tools.py") that is supposed to do the necessary calculation in a straightforward way, according to the guidelines provided in http://www-personal.umich.edu/~mlerner/Pymol/. I've follewed them but the plugin asks for an "APBS binary location". I do not know what a "binary location" is or where to find it. I'm using PDB files converted to PQR files, as indicated in http://www.csb.yale.edu/userguides/graphics/pymol/electro.html., and run the APBS tool selecting a ramdonly chosen "APBS binary location". The program seems to do calculations on the surface of the protein although does not generate any figure representing the results. By clicking on visualization the plugin warms that at least a molecule and a map must be loaded. Is the plugin asking for the calculated electrostatic surface map? Is so, how do I find it? Does it have to be with the "APBS binary location" issue? Well, lots of questions...
Thank you beforehand...
