Other tools

Parameterization

Unfortunately, the majority of problems encountered during electrostatics calculations arise in process of taking a structure from the Protein Data Bank and transforming into a file that can be used by the APBS software. The PDB2PQR service was orginally developed in conjunction with Jens Nielsen and Andy McCammon to address these issues. The service has since evolved and has been completely rewritten by Todd Dolinsky and Nathan Baker. PDB2PQR is able to:

• Fill in missing atoms in the PDB (within reason)

• Add hydrogens to the structure to optimize the hydrogen-bonding network.

• Calculate side-chain pKas

• Assign charges and radii according to one of the following force fields: CHARMM23, AMBER02, or PARSE

• Return the results in PQR format

Please visit the PDB2PQR home page ( http://pdb2pqr.sourceforge.net) for more information, links to available servers, and download options.

Additionally, APBS provides the ability to read plain PDB-format files and assign charges and radii from user-supplied parameter files. These features are described in the READ PARAM command description.

Finally, APBS provides a few other miscellaneous tools for converting and parameterizing structures:

• tools/conversion/qcd2pqr.awk

  Convert a QCD file (UHBD format for a molecule) to PQR format.

• tools/conversion/amber2charmm.sh

  A script which converts a PDB file with AMBER atom names to a PDB file with CHARMM atom names. Useful for preprocessing files before converting with pdb2pqr.

• tools/conversion/WHATIF2AMBER.sed

  A sed script for converting a PDB file with WHATIF atom names to a PDB file with AMBER atom names. Useful for preprocessing files before converting with pdb2pqr. Contributed by Chiansan Ma.

Problem setup

In addition to parameterization of the molecule, there are several common operations which are performed to setup the calculation. This section reviews some of the tools available for these operations.

The following scripts help generate or transform APBS input files:

• tools/manip/psize.py

  Get the dimensions and center of a molecule in PQR format. Very useful for setting up input files (i.e., grid dimensions, lengths, spacings, etc.) for APBS calculations. Written by Todd Dolinsky and Nathan Baker.

• apbs/tools/manip/inputgen.py

  Generate an APBS input file from PQR format data using "suggested" parameters. Also can decouple a parallel calculation into a series of sequential (asynchronous) calculations to be performed on a single processor. Written by Todd Dolinsky and Nathan Baker.

• tools/mesh/mgmesh

  List acceptable grid dimensions/multigrid levels combinations for mg-manual calculations. Written by Nathan Baker

Output data processing

The following tools perform typical analyses of the output data, usually in OpenDX format. These scripts are not meant to be comprehensive; instead, they provide templates for users to generate their own tools.

Data visualization

This section describes the data visualization tools provided with APBS. A more complete discussion of the various ways to visualize APBS output is presented in the Visualization section of this manual.

• tools/visualization/vmd

  This directory contains scripts which facilitate the visualization of APBS data with VMD.

  NOTE: As described in the Visualization section, a much more elegant interface has been developed for APBS and is available from the VMD plugins page.

  The version distributed with APBS was written by Nathan Baker and Dave Sept based on example Tcl scripts by John Stone. The file loadstuff.vmd is the command file to be modified to the users' tastes and loaded into VMD. The file read_dx contains the Tcl functions needed to read the APBS output.

• tools/visualization/opendx

  This directory contains the OpenDX program files (*.net) required to visualize APBS data with OpenDX. In particular, one can visualize single-file potential isocontours (pot.*), single-file potential data mapped onto molecular surfaces (potacc.*), or multiple-file potential data (multipot.*).

Solvent accessibility

We provide a simple program (tools/manip/acc) which calculates molecular volumes, surface areas, and other surface-based properties from PQR-format structural data. Such calculations are often used to determine apolar solvation contributions to binding events, etc. This program has a number of options which can be viewed by running acc with no arguments.

Coulomb's Law and Generalized Born calculations

These utilities are provided for occasional use and are definitely not optimized for speed.

NOTE: Many of these tools will be incorporated into the main APBS executable during upcoming releases!

Eigenvalue analysis

tools/arpack/driver

If APBS is linked with ARPACK (see configure --help), this routine will perform eigenvalue analyses of matrices produced by APBS.

Python development tools

There are a number of example Python tools and wrappers provided in the tools/python directory. These tools all make use of the APBS SWIG wrappers developed by Todd Dolinsky, Nathan Baker, Alex Gillet, and Michel Sanner. The SWIG wrappers are compiled by default during normal installation. The Python scripts which link to the wrappers (and thereby illustrate their use) include:

• tools/python/main.py

  Drop-in replacement for main APBS executable. Only permits sequential runs.

• tools/python/noinput.py

  Similar to main.py, but adds the ability to read input files and PQR files as Python strings and return energies and forces as Python lists. This makes it a very useful tool for working with APBS via Python without dealing with a great deal of file I/O.

• tools/python/vgrid/

  Python wrappers for Vgrid class to allow OpenDX format file I/O in Python scripts