APBSmem version 1.13 released - Nov 06 2013
APBSmem can be run in batch mode from the command line now.
In batch mode, the GUI still appears, but the calculation
will start automatically, and APBSmem will exit upon completion.
Thus you can run APBSmem in scripts.
Run normally (or double-click on the jar file):
java -jar apbsmem.jar
Some users may need to give java more memory:
java -Xms400m -Xmx800m -jar apbsmem.jar
java -jar apbsmem.jar <input-file> <output-directory>
For example, APBSmem comes with the three example calculations
from the APBSmem paper. To run the first example from the command line
in the apbsmem directory:
java -jar apbsmem.jar dist/1_proteinsolvation/1_proteinsolvation.solv.in ../out1
Warning: Gating charge calculations and other calculations with a
the boundary condition in APBSmem set to "Membrane potential",
(or in APBS with the boundary condition set as "bcfl mem",)
will not work with the latest APBS due to a bug. 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)
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. Bug fix release.
Fixes potential 1-3 minute hang before the GUI appears.
Version 1.11.2. 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. Bug fix release.
Fixed a bug with version 1.11 which caused incorrect results when
using the "Step Ion" feature.
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 picking 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 2
without writing your own PQR files by hand.
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.