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APBSmem Changelog

What's new in APBSmem 2.0 Beta

Jan 27, 2015
  • NEW FEATURES:
  • PDB2PQR has been integrated into APBSmem. This allows the user to convert a PDB file to PQR file, alter protonation states and change forcefield parameters from within APBSmem
  • Delta-pKa button has been added to calculate the membrane induced pKa shift of a residue sidechain
  • Ligand salvation energy has been added as new calculation type (ligand must be provided as a mol2 file when converting a pdb to a pqr file)
  • Representations menu allows the user to change the molecule representation from the default ball-and-stick representation to new cartoon representations color coded by side chain protonation state or protein solvation energy
  • Nonpolar energy is now calculated with protein solvation and gating charge calculations (Michael Sanner’s MSMS program must be installed for this function) Different NP models can be selected from the NP models menu. All NP models are based the change in solvent accessible surface area, but these models allow the user to select whether or not to include atoms in the head group region as solvent excluded.
  • Flooding algorithm to draw the membrane around the protein. By using a flood fill method, the membrane will not be drawn in regions separate from the bulk membrane area (such as aqueous pores and cavities). This feature was recently developed and has some limitations. Ensure that the final focus volume encompasses the protein in the x-y plane, and make sure that the grid dimensions and lengths are equal in the x y and z directions.
  • REQUIRED SOFTWARE:
  • APBS 1.4.1, the previous version does not work when the boundary condition in APBSmem set to "Membrane potential"
  • MSMS (optional). Used to calculate solvent accessible surface areas for non polar energy calculations. APBSmem will just calculate electrostatic energies if MSMS is not included.
  • Python 2.7 (optional). Used to run PDB2PQR for PQR creation/modifications.
  • Numpy 1.9 (optional). Used by PDB2PQR to assign parameters to ligands.
  • KNOWN ISSUES:
  • Ligand option during pdb setup will fail if APBSmem is opened by double clicking the icon. Open apbsmem from command line when using ligands. (java -jar )
  • MSMS will sometimes fail when calculating non polar energy when the flooding algorithm is used. This can sometimes be fixed by slightly changing the grid length for the final focus volume.
  • Larger grid dimensions (>129) will cause java to run out of memory open apbsmem from terminal with extra memory allocation when using large grid dimensions. (java -Xms512m -Xmx512m -jar apbsmem.jar)