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]
- 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.
- 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.