# Difference between revisions of "Apbsplugin"

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To the left in '''Molecular Surface''', click '''Show'''. <br> | To the left in '''Molecular Surface''', click '''Show'''. <br> | ||

Tadaaa! | Tadaaa! | ||

+ | Hide it again, now show both ''Positive'' and ''Negative'' Isosurface | ||

== Troubleshooting == | == Troubleshooting == |

## Revision as of 19:19, 6 December 2011

## Contents

## Software requirements

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

Register here, it takes 1 minutes: http://www.poissonboltzmann.org/apbs/downloads

### Windows

Download **APBS.msi** from: http://sourceforge.net/projects/apbs/files/apbs/

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

There is a nice tutorial on the APBS homepage: [1]

For further help, there is a mailing list [2] with the corresponding archive [3]

### Example 1

Read about the protein here: http://www.proteopedia.org/wiki/index.php/3ig7

```
reinitialize
fetch 3IG7, async=0
#load 3ig7.pdb, 3IG7
create cdk2, 3IG7 and polymer
create EFP, 3IG7 and organic and not resn ACE
delete 3IG7
hide everything, all
#h_add cdk2
#h_add EFP
show_as cartoon, cdk2
show_as sticks, EFP
util.cbay EFP
select flexible, byres cdk2 within 3.5 of EFP
show sticks, flexible
util.cbag flexible
disable flexible
zoom cdk2
```

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

Click in **Selection to use**, and write **cdk2**.

Click **Set grid**

Click **Run APBS**

To the left in **Molecular Surface**, click **Show**.

Tadaaa!
Hide it again, now show both *Positive* and *Negative* Isosurface

## Troubleshooting

See: APBS#Troubleshooting

## References and LICENSES

### 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.

Register here, it takes 1 minutes: http://www.poissonboltzmann.org/apbs/downloads

Please acknowledge your use of APBS by citing:

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

Please acknowledge your use of the Holst group software by citing:

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.

Register here, it takes 1 minutes: http://www.poissonboltzmann.org/pdb2pqr/d/downloads

### 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.

Copyright and Terms of Use:

GNU General Public License: http://www.gnu.org/copyleft/gpl.html

```
This version of MALOC is distributed under the following guidelines:
MALOC (Minimal Abstraction Layer for Object-oriented C)
Copyright (C) 1994-2010 Michael Holst
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
```