Welcome to the APBSmem Wiki
- APBS version >= 1.2.0
- APBS is available from http://www.poissonboltzmann.org/. Versions earlier than 1.2.0 will not perform gating charge calculations properly, and may have issues with ion solvation calculations as well.
- Java Runtime Environment version >= 1.5
- Java should already be installed on most modern systems. If not, you can download the Java Runtime Environment from http://java.sun.com/.
- Untar/unzip the archive:
tar xzvf apbsmem-x.xx.tar.gzOR
- Make sure APBS is installed and that it exists on your path. You should be able to run the following command from the APBSmem directory:
- To run APBSmem in most operating systems you can simply double-click on the JAR file, or to run from the command line, type the following:
java -jar apbsmem.jar
Load your protein or molecule by clicking the Browse button and selecting its file. If your file is in PDB format, it needs to be converted to PQR format for APBS. This can be done via PDB2PQR, available at http://pdb2pqr.sourceforge.net/.
The parameters from previous APBS and APBSmem calculations may be loaded by selecting "Load parameters..." from the File menu, and then selecting the *.solv.in file from the previous calculation. Files for the case studies for each of the 3 calculation types -- Protein Solvation, Ion Solvation, and Gating Charge -- are packaged with APBSmem. Please note that input files from previous APBS calculations will not contain any of the membrane-specific APBSmem parameters -- these settings will only be found in .in files written by APBSmem (they are saved as comments at the beginning of each input file).
The Preview button performs a quick estimate using a smaller grid size of 65 x 65 x 65 so that you can position and visualize the membrane. When you have correctly configured your system, click the Run button to perform the full calculation.
To display an isocontour of the electrostatic potential, check the "Draw Potential" checkbox before running your calculation. The textbox to the right of the Draw Potential checkbox allows you to set the isocontour value at which you'd like the surface to be drawn. With the default value of 2, a surface will be drawn at +2 (in red) and -2 (in blue).
Several parameters specific to APBSmem are described below. For an explanation of APBS parameters, see the APBS User Guide at http://www.poissonboltzmann.org/.
- Head group dielectric: Intermediate dielectric for the polar head region.
- Z-position of membrane bottom: The z-position of the bottom of the membrane in angstroms. This parameter should be adjusted to properly position the protein in the membrane.
- Membrane thickness: The membrane thickness in angstroms. Though a search through literature for experimental evidence is recommended, an estimate of the membrane thickness for your protein may be available at the Orientations of Proteins in Membrane database.
- Head group thickness: Thickness of polar membrane head region. If this is set to zero the head group region is not modeled.
- Upper and lower exclusion radii: The radius of the membrane-protein boundary at the upper and lower membrane leaflets in angstroms. This is often used for channels and transporters that have central membrane-spanning cavities.
- Isosurface contour: This parameter determines at what value the dielectric map isocontour is drawn. If set to Protein-Solvent, the transparent gray surface will be drawn at a dielectric value just slightly greater than the protein dielectric. If set to Membrane-Protein, the surface will be drawn at a dielectric between the membrane and protein dielectrics.
- Grid center: This parameter determines the APBS keyword "gcent" and specifies the centering method used for the APBS calculation. If set to Origin, gcent will be set to (0,0,0). If set to Molecule 1, the centroid of Molecule 1 is calculated and used as the grid center.
- Draw potential: If enabled, this option draws the molecular surface colored by a map of the electrostatic potential. The textbox to the right of the Draw potential option sets the value for the positive (red) and negative (blue) extents of the color mapping. For example, entering 2 in this box will set a spectrum where potential values of -2 and below will be blue and +2 and above will be red. Click the "Redraw" button after changing this value to redraw the potential.
Callenberg KM, Choudhary OP, de Forest GL, Gohara DW, Baker NA, Grabe M. (2010) APBSmem: A Graphical Interface for Electrostatic Calculations at the Membrane. PLoS ONE 5(9): e12722. doi:10.1371/journal.pone.0012722
If you have any problems, questions or suggestions regarding APBSmem please post them in the SourceForge forums or contact Keith Callenberg at kmc112 (at) pitt.edu.