# Difference between revisions of "Apbsplugin"

## Software requirements

Register use of the software. This will the authors able to require funding for further development.

MALOC?

### Ubuntu

APBS are in the repository: http://packages.ubuntu.com/search?keywords=apbs
MALOC are in the repository: http://packages.ubuntu.com/search?keywords=libmaloc1

### Compile yourself

If you really want, then see this section: APBS

## Example 1 - Rename of funny atom names

```reinitialize
fetch 3IG7, async=0
```

Open the APBS Tool2.1... plugin. The executable should be found for itself:

Click tab Grid settings. In Calculate Grid Center by Selection, write EFP.
Try clicking Wired Box in top right, and then Show Box, Hide Box, Cylindric Box, Show Box.
Then push Select binding site. In PyMOL, write

```show sticks, binding_site
cmd.disable("binding_site")
hide sticks, binding_site
```

Click tab Receptor. Mark cdk, and click Generate Receptor.
Click cdk2 to the "right", and see where the files are located.
Click tab Ligands. Mark EFP, and click EFP in the Ligand list. Here is the files stored. Click Generate Ligand
Click tab Docking, and click Run Vina. Wait 3-5 minutes, until Writing output ... done.
Click tab View poses, Browse to EFP.docked.pdbqt. Click Load, Show best 10. Experiment with "Display options, and click the candidates"
Congratulations, you did it!

## Troubleshooting

• If the B-factor is ${\displaystyle \geq 100,}$ then APBS doesn't properly read in the PDB file and thus outputs garbage (or dies). To fix this, set all b factors to be less than 100.
```alter all, b=min(b,99.9)
```
The problem stems from how to parse a PDB file. The PDB file originally was written when most people used FORTRAN programs, and so the file format was specified by columns, not by the more modern comma separated value format we tend to prefer today. For the latest on the PDB format see the new PDB format docs.
• APBS has problems, sometimes, in reading atoms with alternate conformations. You can remove the alternate locations with a simple script removeAlt.
• ObjectMapLoadDXFile-Error: as of this writing (9-23-2008) a known problem exists, and the Baker lab is working on it. It is typically caused by the use of directories with spaces in their names under Windows.

### APBS

When using the APBS, you are "obligated" to register your use of the software. This will the authors able to require funding for further development.

Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. doi:10.1073/pnas.181342398

M. Holst and F. Saied, Multigrid solution of the Poisson-Boltzmann equation. J. Comput. Chem. 14, 105-113, 1993.
M. Holst and F. Saied, Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods. J. Comput. Chem. 16, 337-364, 1995.
For PMG (the multigrid solver):
M. Holst, Adaptive numerical treatment of elliptic systems on manifolds. Advances in Computational Mathematics 15, 139-191, 2001. doi:10.1023/A:1014246117321
For FEtk (the finite element solver):
R. Bank and M. Holst, A New Paradigm for Parallel Adaptive Meshing Algorithms. SIAM Review 45, 291-323, 2003. doi:10.1137/S003614450342061

### pdb2pqr

When using the pdb2pqr, you are "strongly encourage" to register your use of the software. This will the authors able to require funding for further development.

### MALOC

Please acknowledge the use of MALOC and FETK by citing:
M. Holst, Adaptive numerical treatment of elliptic systems on manifolds. Advances in Computational Mathematics, 15 (2001), pp. 139-191.

```This version of MALOC is distributed under the following guidelines: