- Please cite: Callenberg, K.M., Choudhary, O.P., De Forest, G., Gohara, D., Baker, N., Grabe, M. (2010). APBSmem: A graphical interface for electrostatics calculations at the membrane. PLoS ONE 5(9): e12722
APBS: Required to use APBSmem
Aug 2014 Update: APBSmem gating charge calculations work once again with the newest APBS release: apbs 1.4.1. Pre-1.4 versions are no longer needed.
version 1.13 released Nov 06 2013
- Version 1.13 is now available. Download APBSmem v1.13.
- APBSmem can now be run in batch mode from the command line or from script: Providing an input file and output directory will cause APBSmem to perform the calculation and exit.
- Usage: java -jar apbsmem.jar <input-file> <output-directory>
- Warning: Gating charge calculations and other calculations with the boundary condition in APBSmem set to "Membrane potential", (or in APBS with the boundary condition set as "bcfl mem",) will not work with APBS 1.4 due to a bug in APBS. Download an older APBS for gating charge calculations. Bugged APBS versions will report the following error somewhere (not necessarily at the end) in the output file: VASSERT: ASSERTION FAILURE! filename /Users/d3x874/apbs/src/generic/vpbe.c, line 200, (thee->param2Flag)
- Version 1.12.
- Fixes a bug in gating charge calculations introduced in version 1.10. The membrane potential was not being applied. Please upgrade if you perform gating charge calculations.
- Additionally, during a run, the progress bar should accurately reflect the amount of work remaining.
- Version 1.11.3, a bug-fix release.
- Fixes a problem which could cause APBSmem to hang for a couple minutes at startup before the GUI appears.
- Version 1.11.2, a bug-fix release.
- Temporary fix for numerous internationalization bugs: The locale is forced to US for now. This should prevent many errors seen in locales which use a comma (,) for the decimal mark. Correct internationalization support should be available in a future release.
- Version 1.11.1, a bug-fix release.
- Fixed a bug with version 1.11 which caused incorrect results when using the "Step Ion" feature.
- Note to international users: If in your locale a comma is used to indicate the fractional part of a number, (e.g.: 1/2 = 0,5) you may need to use version 1.10. Version 1.11 introduced an internationalization bug which we are working to fix.
- Version 1.11
- The current version adds improved support for protein rotations and translations, some UI tweaks and some warnings to insure that user input is sensical.
- Version 1.10 added two tools for ion solvation calculations:
- Menu item Ion -> Create Ion. After specifing a protein (i.e. PQR file 1), you can use the Create Ion tool to place an ion in the system. This will allow you to quickly create or edit the location of an ion for PQR file 2 without writing your own PQR files.
- Menu item Ion -> Step Ion. After specifing a protein for PQR file 1 and an ion for PQR file 2 (by browsing or by creating a ion with the Create Ion tool) you can use the Step Ion tool to run a series of ion solvation calculations, stepping the ion over a number of locations.
- Version 1.09 added a number of tools under the Orient menu which can be used to display and alter the orientation of the protein in PQR file 1:
- Toggle display of the coordinate axes of the membrane or the protein.
- Rotate and center the protein.
- Auto-orient the protein. Auto-orientation is very simplistic and can only work highly symmetric proteins at the moment. It simply aligns the (unweighted) principal axes of the molecule to the membrane axes.