Basic guides to APBS on PyMOL

The following instruction guides you on how to 1. Install and then 2. Run the APBS (Adaptive Poisson-Boltzmann Solver) plugin for PyMOL under Windows.

Installation

Run apbs_i386_setup.exe
The installation process will create the folder apbs immediately under the C:\ drive. You can change the installation directory, but if you choose to do so, make sure that there is no space anywhere in the directory path.

e.g.
OK  C:\apbs
BAD C:\Users\abc\path with gaps
OK  C:\Users\abc\path_without_gaps

Running the APBS

1. Prepare the PQR file from the PDB file of the structure that you want to draw the electrostatic surface potential diagrams of.
   Visit http://nbcr-222.ucsd.edu/pdb2pqr_1.8/
   
   Either input the PDB accession code, or upload a PDB file.
   
   Download the PQR file.
   
2. Launch PyMOL. Firstly, load the coordinates of the structure (.pdb file). Access Plugin -> APBS Tools 2.1.
   
   
   
   
3. Again, make sure that there is not a single gap in any of the directory paths. I imagine APBS was originally developed to run of Linux-type operating systems.
   
   
   
   
   
4. After waiting, the screen should automatically change to the “Visualisation” tab.
   
   
   
5. Voila!
   
   
   
   One can ray trace it but it doesn’t seem to make much difference to be honest (below).
   
   
   
   
   
   
   
6. Note: While running the above procedure for a larger protein (55 kDa) under Windows 8.1 (64 bit), the PC hung with an error message, “computer has stopped responding” or something like that. I feel this is non-sense, because I saw in the task manager that APBS was happily doing its calculation, just taking some time. Besides, I successfully managed to carry out under Windows 7 Home (64bit). So I think it’s Windows 8.1 is mistaking a long calculation to PC being crashed. Reading the following page (http://www.tomshardware.com/forum/61690-63-program-responding-timeout-edit) did not help, unless I missed something.
   
   Update : Using free academic PyMOL 1.3 and APBS 1.2 can successfully complete the process for the 55kDa structure that failed in the above-mentioned setup, which was PyMOL 1.6 with APBS 1.4. Also failed with PyMOL 1.7 (64bit) with APBS 1.4 (32bit or 64bit). All tested under Windows 8.1 Pro 64bit.