PyMOL has a plugin called APBS tool (http://www.pymolwiki.org/index.php/Apbsplugin) that requires three different file inputs:
- APBS binary (apbs.exe)
- APBS psize.py file
- PDB2PQR pdb2pqr.py file
I have installed APBS and have both apbs.exe and psize.py in my C:\APBS directory. PDB2PQR is the problem, I have downloaded http://sourceforge.net/projects/pdb2pqr/files/latest/download (version 2.0.0 for 64 bit Windows) extracted its contents and failed to find any pdb2pqr.py file in the extracted directory. I have also tried downloading pdb2pqr 1.8.0 tarball (.tar.gz) and extracting its contents, as I was informed on a PyMOL users mailing list that it should contain a pdb2pqr.py file and may be more compatible with PyMOL. But this tarball is the source code and must be compiled which isn't possible on Windows 7 to my knowledge.