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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.

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http://www.poissonboltzmann.org/

This would be your most productive method of getting your answer with a chat to their technical help section and support. As for compiling on Windows 7, yes it is possible as long as you have the COMPLETE source code and compilation routine file.

You may come across a failure in the software due to windows 7 NOT accepting unsigned drivers, plus your installing in the root directory which is a bad idea as Win 7, 8 and so on have blocks in place for legacy type installations in the root directory.

Personally I would look into making a change to the installation and see if you can get it to install in the main program files directory or program files x86 if it is 32 bit software.

You may find it necessary to amend the drives security features to allow the installation to take place. Read the Microsoft notes on this before proceeding and double check any coding prior to compiling. If its a Linux / Unix server based system a virtual Ubuntu server dual install may prove to be of some use to you.

This is general information as I have no knowledge of the use or file system the question is about and should be taken as advice. If in doubt talk to the manufacturer and get there help should always be your first port of call.

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