Drug Design Laboratory



Dipartimento di Scienze Farmaceutiche
Università degli Studi di Milano
Via Luigi Mangiagalli, 25
I-20133 Milano - Italy


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VEGA ZZ 2.3.2 for Windows and Linux (Wine)
November 12, 2009

The new VEGA ZZ 2.3.2 release is available for download. The new features are:

  • GriDock: structure-based virtual screening software.
  • PDBQT multimodel trajectory loader (for AutoDock Vina).
  • Real time bump check.
  • Added the feature to save the calculated hydrogen bonds in CSV and DIF formats.
  • SQLite 3 database engine: it allows not only to store molecules, but also their properties that are calculated on-the-fly by VEGA ZZ for faster searches.
  • VEGA command line: now you can extract the frames from a trajectory file (-m Extract option).
  • SketchEl 2D molecular editor.
  • Unselect apolar hydrogens.
  • Calculation of isotopic distribution (isotopic pattern).
  • Support for NAMD 2.7.
  • Experimental Linux support. The setup is able to detect when VEGA ZZ is installed on a Linux/Wine system enabling specific optimizations.
  • Faster memory manager: it allows more responsive feedback.
  • Improved the CTorFind command. For this reason, the syntax was changed.
  • DMSO solvent cluster.
  • CHARMM 36 force field for small molecules.
  • Fix: error report when the Mopac calculation stops for an error.
  • Fix: IFF loader access violation when the file contains H-bond monitors.
  • Fix: Mopac extended command. Now select the correct executable version.
  • Fix: TrjWrite behaviour with invalid handles.
  • Fix: the AutoDockReceptor.c script checks the maximum number to grid points for each dimension and sets it to 61 increasing the grid spacing in order to avoid to exceed the AutoDock/AutoGrid limits.
  • Fix: HyperDrive potential problem in the multithreading kernel (HD_WaitBarrier()) when a large number of CPUs is used.
  • GriDock manual and tutorial.
  • PowerNet plug-in: interface for Java applets.
  • New extended commands: Build3D, MenuEnable, MovieAdd, MovieClose and MovieCreate.
  • New scripts: AutoDockKi calculator.c (evaluate the Ki and the interaction energy of a ligand - receptor complex), AutoDock/Box calc.c (calculate sizes and center coordinates of the box used for docking studies), BuildCoordinate transformation.c (apply the transformation matrix to the atomic coordinates), ExamplesBenzene.htm (build a benzene ring), ExamplesCommand console.htm (control VEGA ZZ by JavaScript), MovieMovie Maker.c (create a move of a spinning molecule), Protein toolsFred2 score.c (calculate the interaction score of a ligand - receptor complex).
  • Updated the gl2ps library to 1.3.3.