Drug Design Laboratory



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


RSS feed


VEGA ZZ 2.3.0 for Windows
December 10, 2008

The new VEGA ZZ 2.3.0 release is available for download. The new features are:

  • Full support for NAMD 2 MD software with integrated graphic interface.
  • InChI loader and saver. Loading an InChI structure without the auxiliary data, it's automatically converted to 3D (VEGA ZZ only). Chirality and E/Z geometry is automatically checked and fixed if wrong.
  • AutoDock 4 PDBQT loader and saver.
  • AutoDock 4 DLG trajectory loader.
  • Mopac loader for geometry in Gaussian Z-matrix format.
  • Command line version: extraction of a molecule from a database (SDF and ZIP).
  • Chiral atom labels.
  • E/Z bond geometry monitors.
  • The PDB loader is now compatible with the alternate locations.
  • Remove apolar hydrogen.
  • Molar refractivity calculation (Ghose & Crippen method).
  • ChemSol plug-in for the calculations of solvation free energies.
  • Improved performances of the Molecule -> Fix menu function. Now it uses a graph-based routine to find the molecules.
  • PowerNet plug-in: added some on-line service (ChEBI, DrugBank, eMolecules, ERRAT 2.0, Google, KEGG Compound, KEGG Drug, MMsINC, NIST Chemistry WebBook, ProCheck, Prove, PubChem, Super Drug, VADAR, Verify3D and WHAT_CHECK).
  •  New values in InfoXML format: chiralatms (list of the chiral atoms), chiralnum (number of chiral atoms), ezbonds (list of the bonds with E/Z geometry), gcmr (Ghose & Crippen molecular refractivity), eznum (number of bonds with E/Z geometry), hbondacc (number of H-bond acceptor atoms), hbonddon (number of H-bond donor atoms), realmols (real number of molecules), rings (number of rings), torflexnum (number of flexible torsions) and tornum (number of torsions).
  •  PropKa: updated to the 2.0 release and the Windows x64 version built by gfortran.
  • New icons in the graphic interface.
  • New InChI copy special data types.
  • Fix: peptide builder window cut when the desktop dpi are more than 96.
  • Fix: Mopac loader and saver when the number of atoms is less than three.
  • Fix: recognition of the Mopac Cartesian .arc files.
  • Fix: PDB saver writing the TER record with residue name length less than three characters.
  • Fix: tube rendering with big molecules and high spline resolution and hardware/software picture rendering.
  • Fix: measure selection in the trajectory analysis tool.
  • Added the chirality information in the IFF/RIFF file format.
  • New system variable: InChI, InChIAux, HbAcc, HbDon, Sequence, TotChiral, TotEZ, TotHeavyAtm, TotHydrog, TotRealMol, TotRing, VlogP.
  • New extended commands: CopyText.
  • New scripts: AutoDockLigand.c (prepare the current molecule to be docked by AutoDock 4), AutoDockReceptor.c (prepare the current molecule to be the receptor usable by AutoDock 4), CalculationCopy properties.c (copy some molecular properties to the clipboard), ClaculationDruglikeness.c (check the druglikeness of a molecule), DatabaseDrugBank SDF fix.c (fix the not standard SDF files from DrugBank), TrajectoryAnim maker.c (generate trajectories that can be rendered in video files), TrajectoryAutomatic quenching.c (perform the automatic quenching of a MD trajectory. New version) and TrajectoryDump energy.c (dump the energy of each frame in a trajectory file). 

Click here to download the new package