APBS for Dummies (Version 0.4.0)

(Acknowledgement: Thanks to Sandeep who provided guidance)

Setup

Download pdb2pqr

Step Through

• pdb2pqr.py –ff=”amber” –apbs-input <filename.pdb> <filename.pqr> [This will generate filename.in]
• prun –n 1 apbs filename.in [This will generate pot.dx]
• Note: Most probably you will get the following error message for APBS 0.4.0:
• PBEparm_check: SDENS not set!
• NOsh: MG parameters not set correctly!
• Error while parsing input file.
• Add the following line into your .in file. [sdens keyword sets the sphere density for the APBS Vacc accessibility object]
• sdens 10.0
• Another way is to edit inputgen.py in the pdb2pqr/src directory
• Add a line anywhere after text += self.getCenter() and before text += "end\n". Note that this line have to be added at two locations in the file.
• text += " sdens 10.0\n"
• Caution: Ensure that your .dx and your .pdb file must not be of the same filename. PyMol can’t differentiate between the 2 of them if they have the same filename even with different extension.