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
- 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. - Launch PyMOL. Firstly, load the coordinates of the structure (.pdb file). Access Plugin -> APBS Tools 2.1.
- 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.
- After waiting, the screen should automatically change to the “Visualisation” tab.
- Voila!
One can ray trace it but it doesn’t seem to make much difference to be honest (below).
- 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.
