APBSmem

Poisson-Boltzmann electrostatics in the membrane

 
APBSmem is a Java-based graphical interface that enables users to perform electrostatics calculations on biomolecules in an implicit membrane environment.  

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    APBS: Required to use APBSmem

Recent news

APBSmem version 1.12 released Oct 05 2012
  • Version 1.12 is now available. Download APBSmem v1.12.
    • 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.