Drug Design Laboratory
News > Software projects > VEGA ZZ > History

History

M1 muscarinic receptor - acetylcholine complex

In this section, you can find the list of the features inplemented in VEGA ZZ through the years.

  Release ZZ 3.0.1 (16/11/2012)
   
  • Mol2 database management.
  • New ATDL routines for version 4 templates. The old templates continue to use the previous routines.
  • Added the support for Mopac 2012.
  • New script: DatabaseForce field check.c, DockingAPBS binding energy.c, DockingPLANTSReceptor.c, DockingPLANTSPatch bin 1.1.c.
  • Updated DockingPLANTSDocking.c script to manage the side chain flexibility.
  • Fix: access violation when you close a single database.
  • Fix: copy to clipboard of AMMPInteraction energy.c script.
  • Fix: SQL queries.
  • Fix: trajectory file lock when the molecule is closed.
  • Fix: dialog update adding hydrogens and ions.
  • Fix: PSA calculation of a selected set of atoms.
  • New system variable: Mol.
  • New extended commands: DbReOpen, DbUpdate.
      
  Release ZZ 3.0.0 (21/06/2012)
   
  • Saver, DB engine, copy special, and InfoXML format updated to support InChIKey.
  • DB engine updated to support ODBC and Microsoft Access databases.
  • Copy to clipboard 2D sketches (copy special).
  • New popup menu sensible to the context.
  • Save the picture of 2D sketches.
  • 2D preview in SMILES editor and database explorer.
  • Optical structure recognition (provided by OSRA).
  • Customizable database reports.
  • Editing of database fields.
  • PSA with color smoothing (OpenCL powered).
  • Color by flexible torsion (normal and AutoDock).
  • Automatic shutdown at the end of the calculation.
  • New graphic interface with magnetic windows.
  • Possibility to click on windows entirely covered by other ones.
  • User-defined window layouts.
  • Ethanol cluster for solute solvation.
  • AutoDock Vina is now included in the package and it's fully supported.
  • Automatic update check and setup.
  • REBOL installation no more required.
  • Fix: Mopac .arc file recognition.
  • Fix: SQLite update procedure.
  • Fix: PSA calculation.
  • New system variables: ConfigDir, ConLines, InChIKey, IsWOW64, MassAct, ScriptsDir, WksLocked.
  • New extended commands: BuildPept, ConGetLine, DbLock, OpenEx, SaveImg2D, SecStruct, SetLastFileName, Smiles.
  • New scripts:
    - Calculation\XLOGP2.
    calculate the logP by XLOGP V2 method.

    - Database\SMILES to database.c
    convert a file containing SMILES strings to a database.

    - Docking\PLANTS\Rescore ChemPlp.c
    - Docking\PLANTS\Rescore Plp.c
    - Docking\PLANTS\Rescore Plp95.c
    evaluate ligand - receptor interactions by different PLANTS scoring functions.

    - Docking\Vina\Docking.c
    Vina graphic interface.

    - Docking\Vina\Ligand.c
    prepare the ligand to be docked by Vina.

    - Docking\Vina\Receptor.c
    prepare the receptor to be docked by Vina.

    - Docking\Vina\Virtual screening.c
    complete easy-to-use virtual screening system based on Vina.

    - Docking\X-Score.c
    evaluate ligand - receptor interactions by X-Score.

    - Interaction surface\CHARMM interaction surface.c
    show the ligand-receptor interaction surface using the CHARMM force field.

    - Interaction surface\Lipophilic interaction surface.c
    show the ligand-receptor lipophilic interaction surface.

    - Interaction surface\MEP interaction surface.c
    show the ligand-receptor electrostatic interaction surface).

    - Interaction surface\MLPInS color ramp.c
    normalize the color ramp of surfaces calculated by MLPInS interaction surfaces.c

    - Interaction surface\MLPInS interaction surfaces.c
    show the ligand-receptor MLPInS interaction surface

    - Movie\Sec. structure anim.c
    create a movie changing the secondary structure.

    - QSAR\Automatic linear regression.c
    generate all possible regression models.

    - QSAR\Linear regression.c
    perform multiple linear regressions.

    - Trajectory\DCD fix for VMD.c
    patch buggy DCD files generated by pre-3.0.0 VEGA ZZ releases.
     
  • New batch files: Namd.cmd (NAMD command line interface), NamdClean.cmd (clean the directory removing useless files and keeping NAMD results), NamdMulti.cmd (perform multiple NAMD calculations considering all input files in a given directory).
  • AutoDock 4 and AutoGrid 4 were compiled by gcc 4.6.3 for x86 and x64 Windows with a significant performance improvement (from 2 to 3 time faster than the previous build made by gcc 3.4.5).
  • AutoDock Vina 32 and 64 bit version built by gcc 4.6.3 are now included in the package. Vina 64 bit is up to two time faster than the original 32 bit version.
    - gcc and gfortran 4.6.3 were used to update both 32 and 64 bit executables (AMMP, ChemSol2, ESCHER NG, Fpocket, HyperDrive, InChI, Mopac7, Predator, PropKa, VEGA command line). 
  • Updated gl2ps library to 1.3.6.
  • Updated InChI library to 1.03.
  • Updated REBOL/View to 2.7.8.
  • VEGA ZZ in now compiled by RAD Studio XE.
  • Support of Wine emulation layer discontinued.
  • VEGA command line for Linux includes binaries for both x86 (32 bit) and x64 (64 bit) operating systems in a unique package. Now, the same package contains also: AMMP, ESCHER NG, GriDock, Mopac 7 and SQLite.
     
  Release ZZ 2.4.0 (4/10/2010)
   
  • OpenCL acceleration for surface and Virtual logP calculations. The OpenCL support is available for all VEGA releases (ZZ for Windows x86, command line for Windows x86, x64 and Linux x86, x64).
  • SMILES loader, saver and editor.
  • Bond length check.
  • New interaction analysis tool.
  • MassTools: mass spectrometry plug-in (available in a separated setup) for database searches to identify molecules by monoisotopic mass and isotopic distribution.
  • Pockets: plug-in for the detection of the protein pockets. It uses the fpocket software developed by Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery.
  • MDL Mol and SMILES copy to clipboard function.
  • Possibility to set the probe radius when the volume or the volume diameter is calculated in the trajectory analysis tool.
  • Selection of nucleic acid backbone.
  • 10 bit output for each color channel (special graphic card and monitor are required).
  • Mopac interface updated.
  • Fix: HyperDrive DFT routines when executed by more than two threads.
  • AutoDock 4.2.3 is now included in the package (Win32, Linux x86 and Linux x64 versions).
  • New system variables: IsoDist, Smiles.
  • New extended commands: AtmInvChirality, BeginCalc, DbGetRowID, EndCalc, IsoDist, Score, SaveMolDlg, SelProx, SrfRename, TrjCurEne, Turbo, UndoPush, UnSelProx.
  • New scripts: AutoDock DLG to PDB Multimodel (convert the AutoDock DLG output to a PDB multimodel file), Protonation fix.c (fix the protonation state), SDF metadata extractor.c (extract the metadata from a SDF file), Stereoisomers.c (build all possible stereoisomers), Subset creator.c (create a database including a molecule subset from another database).
  Release ZZ 2.3.2 (11/11/2009)
   
  • 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 Wine 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 AutoDock\Receptor.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: AutoDock\Ki 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), Build\Coordinate transformation.c (apply the transformation matrix to the atomic coordinates), Examples\Benzene.htm (build a benzene ring), Examples\Command console.htm (control VEGA ZZ by JavaScript), Movie\Movie Maker.c (create a move of a spinning molecule), Protein tools\Fred2 score.c (calculate the interaction score of a ligand - receptor complex).
  • Updated the gl2ps library to 1.3.3.
  Release ZZ 2.3.1 (08/01/2009)
   
  • Added the support to Mopac 2009.
  • Fixed the resize problem of the select segment/molecule window.
  • Small bug fixes.
  Release ZZ 2.3.0 (11/12/2008)
   
  • 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: AutoDock\Ligand.c (prepare the current molecule to be docked by AutoDock 4), AutoDock\Receptor.c (prepare the current molecule to be the receptor usable by AutoDock 4), Calculation\Copy properties.c (copy some molecular properties to the clipboard), Claculation\Druglikeness.c (check the druglikeness of a molecule), Database\DrugBank SDF fix.c (fix the not standard SDF files from DrugBank), Trajectory\Anim maker.c (generate trajectories that can be rendered in video files), Trajectory\Automatic quenching.c (perform the automatic quenching of a MD trajectory. New version) and Trajectory\Dump energy.c (dump the energy of each frame in a trajectory file).
  Release ZZ 2.2.0 (10/04/2008)
   
  • Undo/redo functions.
  • Fasta loader with automatic conversion from 1D to 3D.
  • Mopac cartesian loader and saver.
  • PDB Large saver. The PDB Large file format was implemented in order to save molecules with more than 99999 atoms and is full compatible with the NAMD package.
  • Gromacs TRR trajectory loader & saver.
  • Peptide builder.
  • Protein secondary structure editing.
  • Bond length editing.
  • Added the automatic pair selection (Similar pairs and All pairs) in the similarity tool by a new popup menu.
  • Selection of the unconstrained atoms.
  • Automatic definition of the protein torsions (Omega, Phi and Psi) in the selection tool.
  • Added the -t and -u options to the command line version to change the protein secondary structure and to add the side chains to a protein.
  • Improved Mopac2007 support.
  • Automatic activation of the OpenGL V-sync. You don't need more to enable it in the graphic card control panel to improve the animation quality.
  • ISIS/Draw plug-in: now it checks if the hydrogens are already present in the ISIS/Draw structure and if this condition is true, no hydrogen is added. The Force add hydrog. menu item allows to skip this check.
  • ISIS/Draw plug-in: the chirality is correctly kept during the molecule transfer from ISIS to VEGA ZZ.
  • New atom picking routine to avoid the performance issue of the OpenGL selection buffer implemented in the ATI drivers.
  • The Live CD Creator can install VEGA ZZ on a pen drive. Now it's possible to build a bootable CD with the VEGA ZZ plug-in for BartPE and PeBuilder.
  • Molecular docking tutorial with VEGA ZZ and Fred.
  • Added the support for the Asus Eee PC sub-notebook.
  • Fix: IFF loader & saver when the molecule contains centroids.
  • Fix: add hydrogen by bond order routine.
  • New script: PDB ren export.c (export the molecule in PDB format renumbering the atoms).
  • Updated VEGA SE screen saver (1.1.0.1).
  • VEGA On-line package and manual.
  Release ZZ 2.1.0 (10/10/2007)
   
  • CIF and mmCIF loader and saver.
  • MDL Extended Molfile (V3000) loader and saver.
  • Info XML saver.
  • mmCIF multi-model trajectory loader.
  • ISIS/Draw plug-in.
  • Stride plug-in.
  • Changes in bond dialog: added the function to replace the conjugated bonds with partial double bonds in aromatic rings.
  • The graphic interface is now COM Control 6.0 compliant.
  • Printable manual.
  • Added the -q option to the command line version to assign the bond order.
  • Fix: start-up problem of the latest Mopac 2007 releases.
  • Fix: small problem in the activation wizard.
  • Fix: client area in sizeable windows when Windows is configured with big fonts (> 96 DPI).
  • Fix: nanotube REBOL script.
  • New extended commands: Activate, FixArom, GraphAddEx, GraphType, UpdateLastFile.
  • New scripts: Database volume.c (calculate the volume of each molecule in the database), XYZ import.c (customizable XYZ loader).
  • Updated the CPU detection to recognize the new CPUs.
  • Updated the tutorial section.VEGA SE screen saver.
  Release ZZ 2.0.8 (06/03/2007)
   
  • Conformational search (grid scan, random and Boltzmann jump).
  • Cluster analysis of the trajectory files (cluster by coordinates, by torsion and by torsion RMSD).
  • Mol2 multi-model trajectory saver.
  • X-Plor PSF loader.
  • ChemSol loader and saver.
  • CML 1.0 & 2.0 loader and saver.
  • PQR saver.
  • CHARMM 22 force field for AMMP.
  • Improved the rendering speed of solid surfaces with OpenGL 1.5 compliant graphic cards (2x time faster).
  • Mopac 2007 support (not included in the package).
  • PSF saver totally rewritten and new improper angle detection.
  • HyperDrive K8 for AMD Opteron, Athlon 64/FX and Sempron 64 CPUs.
  • 64 bit version of AMMP, ESCHER NG, InpMerge, PropKa, Top2Tem, Vega command line version, WarpBench, WarpGate, WarpKeyGen and WarpTel for Windows XP Professional x64 Edition, Windows Server 2003 x64 Editions and Windows Vista x64 Editions.
  • Slow motion function converting a trajectory to a video stream.
  • Gasteiger charges and the ATDL engine use the new parallel code.
  • ATDL template cache for a faster atom typing.
  • Added the possibility to compute manually the total charge in the Mopac dialog window.
  • PowerNet plug-in: script description feature.
  • Tutorials for most common molecular modelling problems.
  • Fix: Excel driver.
  • Fix: Gromos/Gromacs loading of very big files.
  • Fix: connectivity merge.
  • Fix: WarpGate access violation if an invalid host name is found in the configuration file.
  • Auto-installation utility for the license file (LicInst).
  • Updated the CPU detection to recognize the Intel Core 2 CPUs.
  • AMMP 2.2.0.
  • WarpGate 1.1.
  • New extended commands: AmmpSetFF, AmmpUpdateFreq, CTorClear, CTorGet, CTorFind.
  • New system variable: TotCTor.
  • New scripts: Database logP.c (calculate the logP for each molecule in the database), SDF export.c (export a trajectory in a SDF database), Dump backbone torsions.c (dump the phi and psi backbone torsion values).
  • InpMerge: utility to merge the CHARMM/NAMD parameter files.
  • Italian localization of the setup procedure.
  • Updated the gl2ps library to 1.3.2.
  • Updated the libbzip2 library to 1.0.3.
  • Updated the ziplib library to 1.0.1.
  • Updated the zlib library to 1.2.3.
  • Demo music remastered with surround effects.
  Release ZZ 2.0.7 (18/09/2006)
   
  • Molecular mechanics provided by AMMP (Another Molecular Mechanics Program).
  • Host control system for remote jobs.
  • AMMP loader and saver.
  • CPMD XYZ loader and saver.
  • Mol2 and MDL Mol multi-model trajectory loader.
  • AMMP - MoM atomic charge calculation.
  • SVG image output.
  • Fix: Gl2vrml library memory leak.
  • Fix: PROPKA bug when the path of temporary directory contains dots.
  • Fix: RIFF/IFF charge and potential chunk bug.
  • Fix: client area reduction of resizable windows when the window title bar height is greater than 14 pixels.
  • Fix: Connectivity merge.
  • Fix: Excel driver.
  • Fix: SDF database engine.
  • Fix: Lock of the HyperDrive parallel threads after preferences change.
  • New extended commands: AmmpSend, AmmpSendMol, AmmpStartCalc, SoundEffects.
  • New system variable: SoundEffects.
  • New scripts: 2D to 3D.c (convert a structure from 2D to 3D), Aromaticity fix.c (Fix the bond order in aromatic rings), CSSR SOMFA export.c (export the molecule in SOMFA readable format), Database 2D to 3D (convert a database from 2D to 3D), Database to 0D.c (convert a database from nD to 0D), Dipole.c (compute the dipole momentum with AMMP), GraphApp demo.c (Demo of the GraphApp GUI library), InChI convert.c (IUPAC InChI converter), Interaction analysis.c (evaluate the interaction energy between two molecules), Neural network.c (use the AMMP's neural network to reconstruct the 3D geometry), Rigid docking.c (genetic algorithm rigid docking), Zero coord.c (Place the atoms at the specified coordinates).
  • WarpBench parallel linpack benchmark.
  • WarpGate encrypted tunnelling service for Linux and Windows.
  • WarpKeyGen encryption key generator. 
  • WarpTel encrypted telnet server for Windows.
  • Updated the Gl2ps library to 1.3.1.
  • Updated REBOL/View to 1.3.2.
  • Live ! distribution. It doesn't requires the installation and VEGA runs directly from the CD-Rom drive.
  Release ZZ 2.0.6 (28/02/2006)
   
  • PROPKA plug-in for protein pKa calculation (thanks to Jan H. Jensen).
  • Added the capability to add the atom charges using a fragment/residue database containing pre-computed charges.
  • Gaussian input loader and saver.
  • Gaussian output loader.
  • RIFF, RIFF 64 bit and IFF 64 bit molecule/trajectory loader and saver.
  • New algorithm based on the bond order to add hydrogens. This is useful for databases and 2D structures.
  • The DCD reader and writer is now compatible with the trajectories containing the cell information.
  • Add fragment with automatic residue number increment.
  • Preferences dialog box.
  • Introduction to the VEGA Graphic Language (VEGA GL).
  • Added Edit -> Remove -> Graphic objects menu item.
  • Updated PDB download for the new RCSB Web site.
  • Fix: molecule view loading files overriding the Z-clip plane.
  • Fix: Mopac 7 bug due to g77 3.4.2.
  • New extended commands: VglBegin, VglColor, VglColorRGB, VglDisable, VglEnable, VglGroupBegin, VglGroupEnd, VglGroupHide, VglGroupRemove, VglGroupShow, VglEnd, VglInit, VglLabel, VglLineWidth, VglLoadIdentity, VglNormal, VglPointSize, VglPopMatrix, VglPushMatrix, VglRadius, VglRadius3, VglRotate, VglScale, VglTranslate, VglVertex.
  • Top2tem: utility to convert CHARMM topology files (.top) to VEGA template files for charges (.tem).
  • Updated SendVegaCmd to 2.6.
  Release ZZ 2.0.5 (5/12/2005)
   
  • C script engine based on Tiny C compiler.
  • Mopac 7.01-4 is now included in the package.
  • Ramachandran plot plug-in (RamaPlot).
  • Customizable Cartesian axis.
  • VRML 2.0 and POV-Ray  output (powered by Gl2Vrml library).
  • New in the database explorer: support for the file drag & drop, molecule list save and clipboard copy functions.
  • Selectable multisample anti-aliasing.
  • Configuration of human interface devices (HID).
  • Fix: small SDF database remove molecule bug.
  • Fix: trajectory gyration radius calculation.
  • Fix: dotted PSA surface calculation apolar and polar area value.
  • Fix: access violation saving the surfaces.
  • Fix: H-bond donor surface calculation.
  • Fix: removed the artefacts in transparent surface visualization.
  • Fix: HyperDrive handle release in SMP mode.
  • Fix: bond angle adding the hydrogens to the water molecules.
  • Fix: snapshot corruption with ATI graphics card when the multisample anti-aliasing is enabled.
  • Fix: first atom skipping in xyz loader.
  • New scripts: ActiveSync VRML send.c (convert the molecule to VRML and send it to the mobile device using ActiveSync), CML export.c (export the current molecule in Chemical Markup Language), CSV export.c (export the current molecule in Comma Separated Values format), Color RasMol.c (color the molecule using the RasMol color scheme), Color VMD.c (color the molecule using the VMD color scheme), E-mail PDB send.c (send a molecule in PDB format as e-mail attachment), Electrostatic energy.c (evaluate the electrostatic energy), HIS protonation.c (check the histidine protonantion state calculating the hydrogen bond energy), IrDA VRML send.c (convert the molecule to VRML and send it to the mobile device over an infrared link), Move hydrogens to end.c (move the hydrogens at the end of the atom list), Ramachandran.c (perform the Ramachandran analysis of a MD trajectory).
  • New extended commands: EneParGet, EneParSet.
  • New system variables: MsAA, WinHandle.
  • How-to manual section.
  • Updated ClustalX to 1.8.3.
  • Updated the Gl2ps library to 1.2.6.
  Release ZZ 2.0.4 (29/06/2005)
   
  • Added the capability to read Mopac 2000 .arc files.
  • Fix: EAccessViolation error with non-european Windows versions.
  • Fix: Mol2 loader with FLEXX files.
  Release ZZ 2.0.3 (21/06/2005)
   
  • Automated bug report procedure.
  • VEGA ZZ is now compatible with Windows 95.
  • Added the capability to un/select and remove waters without hydrogens.
  • Fix: SrfCalc command.
  • Fix: ESCHER NG output recognition.
  • Fix: potential division by zero loading DCD files.
  • Fix: .car file merge.
  • New extended commands: Volume.
  • New system variables: FlexTor.
  • All DLLs are rebuilt with MinGW 3.1, because the release 4.0 generates wrong SSE code for the Pentium 4 target.
  • REBOL/View 1.3 script engine.
  Release ZZ 2.0.2 (24/05/2005)
   
  •  Trajectory file converter with cut/skip frame and atom remove capabilities.  The supported formats are CHARMM/NAMD DCD, PDB and Gromacs XTC.
  • Video stream encoder: the MD trajectory can be converted into a video animation using the Microsoft Multimedia System (AVI file format) or the built-in MPEG-1/2 encoder (mpg and VOB files).
  • Exclusion of atoms in the trajectory analysis.
  • TINKER XYZ loader.
  • Added the support for DCD trajectories with atom fixing.
  • Hydrogen bond finder and energy evaluation with CHARMM force field.
  • H-bond acceptor and donor surface calculation. 
  • Selection of the superficial atoms that are solvent accessible.
  • The atoms can be colored by the property to accept or donate H-bonds.
  • Graph Editor: DFT frequency spectrum analysis, DFT high frequency noise reduction, derivative calculation and label change capability.
  • Automatic selection of the MOPAC executable based on the number of heavy atoms and hydrogens. MOPAC versions for molecules with 50/100/300 heavy atoms and 100/200/600 hydrogens are included in the package.
  • Added the anti-alias function (4x and 16x) when you save the image with the software rendering engine.
  • Added Inherit residue name option in the Add fragment/s dialog.
  • The default window refresh is now set to slow mode for more graphic card compatibility.
  • Added the possibility to change the animation frame rate and the animation base timing.
  • Removed the 2 Gb file size limit of trajectories and databases. The theoretical maximum file size is now 16 Exabytes.
  • Increased performances of the database engine. Now it's possible to manage SDF files containing millions of structures.
  • Fix: Graphic corruption for non-Matrox cards.
  • Fix: Broto/Moreau template. Now the phenolic oxygen atom type is correctly assigned.
  • Fix: Ring detection in the add hydrogens function.
  • Fix: csv, Insight and Quanta surface save procedure.
  • Fix: MDL mol bond type attribution.
  • Fix: Mol 2 loader element recognition.
  • Fix: access violation closing the console.
  • Fix: access violation closing the Graph Editor.
  • Fix: access violation closing databases.
  • Fix: TIFF image saver.
  • Fix: Windows 9x license management.
  • Updated & fixed several scripts.
  • New scripts: Aminoacid selector.r (show the aminoacids by selection and/or chemical/physical properties), Benzene.bat (build a benzene ring using the extended commands), Enantiomerizer.r (convert a trajectory file into the enatiomer one), Ftp put.r (copy a molecule from the workspace to a remote host via FTP), Graphite.r (build graphite planes), Nanotube.r (build nanotubes), Remove apolar hydrogens.r.
  • New extended commands: AssignBndOrd, AtmAdd, AtmBeginUpdate, AtmBond, AtmDelete, AtmEndUpdate, AtmFind, AtmGet, AtmSet, ConnBuild, ConnDestroy, Cursor, DbPut, GraphActivate, GraphBeginUpdate, GraphDerivative, GraphEndUpdate, GraphExcel, GraphMaximize, GraphMinimize, GraphNR, GraphPrint, GraphRestore, GraphSpectrum, GraphToClip, TrjClose, TrjCreate, TrjSave, TrjWrite.
  • New system variables: Formula, ConDocked, Mass.
  • Updated the FAQ section.
  Release ZZ 2.0.1 (20/12/2004)
   
  • Now it's possible to export the molecules directly in Microsoft Excel.
  • Slice selector.
  • The Graph Editor can export the data to Microsoft Excel.
  • Fix: corruption of Z-buffer in stereo view (active glasses).
  • Fix: Windows 9x host detection.
  • Fix: ESCHER NG surface loader.
  Release ZZ 2.0.0 (15/11/2004)
   
  • Introduction of the HyperDrive technology for an incredible computational speed thanks  to its linarized and prallelized  code. It uses the full power of your multiprocessor system !
  • The surface calculation is included in the HyperDrive library. The computational speed is increased to  about 40x.
  • The trajectory analysis takes full advantages of multiprocessor systems with a tremendous calculation speed-up.
  • The HyperDrive includes fast linear routines for the topology calculation and so the PSF file generation is about 20 time faster.
  • The MLP/Virtual logP calculation is now included in all VEGA versions. 
  • Load/save CRT crystallographic files used at the Indiana University Molecular Structure Center (IUMSC).
  • Gyration radius calculation (Info & trajectory analysis).
  • Fix: MEP surface calculation.
  • Added the capability to read Mac ASCII files without conversions. 

VEGA ZZ 2.0.0 updates:

  • New graphic interface.
  • Draggable console, menu and tool bars.
  • Improved graphic performances thanks to the new lighting engine and the possibility to mix the display modes.
  • Fast solid and mesh surface calculation (HyperDrive powered).
  • Enhanced surface color capabilities with customizable gradients.
  • Multiple surface management.
  • Tube and trace visualization modes.
  • Customizable fonts.
  • Support for stereo devices (shutter and anaglyphic glasses).
  • Support for distributed OpenGL rendering (WireGL). 
  • Color settings. 
  • Swap bonds and change angle functions.
  • Improved mouse control and extended move function.
  •  Add aminoacid side chains function.
  • Improved functions in solvent cluster dialog.
  • Enhanced image rendering capabilities: now it's possible to choose  the rendering engine, the image size and the effects/filters to apply.
  • Vector rendering: you can export  the view in LaTex, PDF, PostScript and Encapsulated PostScript.
  • New print engine: now it's possible to hard copy the OpenGL window at full printer resolution for an incredible quality.
  • Check for aminoacid chirality, peptidic bond geometry (cis/trans), missing aminoacids and ring intersections.
  • Add atom and Add fragment dialogs: added the possibility to choose where to put  the atoms in the atom list.
  • Expanded configuration parameters for RMSD calculation.
  • Added Data Interchange Format (DIF) loader and saver in the GraphEd. This feature allows better data import in Microsoft Excel.
  • Now the GraphEd allows to select the energy type to read from NAMD output.
  • New extended commands: BackColor, Light, LightAmb, LightAmbColor, LightCur, LightCurDifCol, LightCurEn, LightCurPos, LightCurSpecCol, LogoPos, LogoScale, MatShiny, MatSpecular, MatVectSpec, MeshLoad, MusicPlay, MusicStop, mTbStandard, mTbTools, Shutdown, SrfAlpha, SrfAlphaVal, SrfColorGrad, SrfCur, SrfDotSize, SrfGrad, SrfGradAutoRng, SrfGradRange, SrfRemove, SrfRemoveAll, SrfVisible, TraceProp, TubeProp.
  • New system variables: BackColor, LastFileName, SaveDir, Light, LightAmb, LightAmbColor, LightCur, LightCurEn, LightCurDifCol, LightCurSpecCol, LightCurPos, LogoPos, LogoScale, MatShiny, MatSpecular, MatVectSpec, SrfCur, SrfName, SrfType, SrfVisible, SkyBoxEnabled, SkyBoxName, SkyBoxOffsetX, SkyBoxOffsetY, SkyBoxRotX, SkyBoxRotY, SkyBoxRotZ, TotBond, TotChain, TotImp, TotRes, TotSeg, TotSrf, TotSrfDot, TotSrfTri, TotTor.
  • The source code is now compiled with Borland C/C++ Builder 6.
  • More computational power thanks to the Borland fastmath library.
  • WinDD 1.5. 
  Release 1.5.1 (16/12/2003)
   
  • Chem3D loader.
  • Accelrys archive file (.arc) support in the trajectory analysis.
  • Capability to add the hydrogens.
  • RMSD calculation in trajectory analysis.
  • CHARMM lipid and GRID force field templates.
  • POPC lipid bilayer cluster in crystal and solid phase. 
  • Fix: energy interaction evaluation.
  • Fix: PSF X-Plor file saver. Now is full compatible with NAMD.
  • Fix: NAMD 2.5b2 & 2.5 output format detection.
Windows/OpenGL updates:

  • ESCHER NG and ESCHER NG Plugin: protein-protein and DNA-protein docking system.
  • Database engine for directory, sdf and zip files.
  • Complete 3D molecular editor with fragment libraries (Add fragment function).
  • Multiple workspaces.
  • Remove residue/s dialog box.
  • Molecule place dialog box.
  • Added the capability to show the worst energy interacting residues with biomacromolecule (Evaluation of the interaction).
  • Fix/merge molecules.
  • Multiple Mini Editor and Graph Editor windows.
  • Now the centroids can be updated dynamically or kept fixed.
  • The residue renumbering is now available for all atoms and for the selected atoms only.
  • Fixed single atom remove function.
  • Changed the keys to control the mouse function (R = rotation, S = scale, T = translation).
  • New extended commands: AddIons, AddHydrog, DbClose, DbCreate, DbGet, DbGetId, DbInfo, DbOpen, GraphSetCur, RemAtoms, WksChange, WksLock, WksNew, WksNext, WksPrev, WksRem, WksRemAll, WksRemCur, WksSetName, WksUnLock.
  • New system variables: GraphID, WksCurName, WksCurNum, WksTot.
  • Updated Fmod DLL to 3.70.
  • New demo music "Rainstorm Cloudburst Mix" by Chris Hülsbeck.
  Release 1.5.0 (24/06/2003)
   
  • PDB 2.2 loader and saver.
  • Experimental PSF X-Plor topology saver.
  • Improved GAMESS support. Now VEGA reads the minimized structures and the atomic charges.
  • Added the capability to read the connectivity and the bond types of Alchemy, CSSR, MDL Mol,  Mol2, PDB (including all subformats), QMC and IFF file formats.
  • Ultra fast connectivity calculation routine.
  • Now IFF and PDB file formats support the atom constraints.
  • Read & write substructure record in Mol2 file format.
  • New trajectory file formats: Quanta conformational search (CSR), ESCHER Next Generation solutions.
  • Added the lipole measure (Broto & Moreau, Ghoose & Crippen) in the trajectory analysis.
  • Support of multiple chains in IFF file format.
  • Bond, CFF91, CHARMM 22 for nucleic acids, CHARMM 22 for proteins, H-bond, MM2, MM3, force field templates.
  • The atom type length is expanded from 4 to 8 characters trough the 64 bit technology (e.g. Tripos atom types). 
  • Added acetone, ammonia, chloroform, dicloromethane, formaldehyde, methane, methanol octanol-water solvent clusters.
  • New specifications for IFF (1.3), PDBA (1.1), PDB FAT (1.1) file formats.
  • Fix: ATDL engine.
  • Fix: IFF multi-segment saver.
  • Fix: trajectory analysis water exclusion routines.
  • Fix: angle between two planes in trajectory analysis.
  • Win32: basic 3D molecular editor with add, remove, change atom capability and bond manipulation (add, remove, change, connectivity rebuilder and bond type finder).
  • Win32: molecular similarity toolbox (molecular superimposition).
  • Win32: change torsion dialog box.
  • Win32: solvent cluster builder.
  • Win32: add ions function (based on Sodium source code developed by Alexander Balaeff).
  • Win32: merge file function. You can merge two files specifying the parts to keep or discard (e.g. coordinates, atom types, atomic charges, etc).
  • Win32: ClustalX plugin.  It allows to integrate molecular biology tools (ClustalX and NJPlot) in the VEGA environment.
  • Win32: atom constraints dialog box for dynamics simulations (e.g. NAMD).
  • Win32: 3D interactive monitors for distance, angle, torsion, angle between two planes.
  • Win32: world relative translation and rotation of each molecule.
  • Win32: open/save in selection tool (trajectory analysis).
  • Win32: select molecules and select segments dialogs.
  • Win32: remove molecules and remove segments dialogs.
  • Win32: remove invisible atoms.
  • Win32: fix/merge segments.
  • Win32: color by fixing value.
  • Win32: labels by fixing value, residue, residue name and residue number.
  • Win32: show/hide atoms by molecule and improved atom selection.
  • Win32: invert Z coordinates function in order to obtain the enantiomer.
  • Win32: apply 3D transformation to coordinates.
  • Win32: now it's possible apply the force field and the atomic charges to all atoms, and to active (visible) atoms only.
  • Win32: event logging in PowerNet plugin.
  • Win32: changed extended commands: Charge, ForceField.
  • Win32: new extended commands: Angle, Distance, Merge, PlaneAng, Torsion, TrjGraphEne.
  • Win32: new system variables: TotActAtm, TotMol.
  • Win32: updated DevIL DLLs to 1.6.5.
  • Win32: new demo music "Giana Sister (Machinae Supremacy Remix)" by Chris Hülsbeck.
  Release 1.4.3 (11/12/2002)
   
  • Alchemy loader & saver.
  • MDL Molfile saver.
  • CSV and Raw surface format.
  • Gromacs .xtc support for the trajectory analysis.
  • Multi-model PDB support for the trajectory analysis.
  • ILM calculation in the trajectory analysis.
  • The IFF file format was expanded in order to support the surface maps.
  • Win32: new geometry transformation engine.
  • Win32: added By segment coloring method.
  • Win32: surface calculation for selected atoms.
  • Win32: trajectory analysis for selected atoms.
  • Win32: interactive selection of the conformations trough the graph editor.
  • Win32: added the Data De/compressor Engine support in the graph editor.
  • Win32: now the graph editor supports Gromacs log files.
  • Win32: REBOL/View instead of REBOL/Core scripting language. 
  • Win32: new extended commands (BioDock, GraphAdd, GraphCalc, GraphClose, GraphDelete, GraphGet, GraphLabelX, GraphLabelY, GraphLoad, GraphNew, GraphOpen, GraphSave, GraphSet, GraphTitle, GraphWin, MonitorPower). 
  • Win32: new system variables (CPUs, GLRenderer, GLVendor, GLVersion, GraphLabelX, GraphLabelY, GraphPoints, GraphPosX, GraphPosY, GraphSizeX, GraphSizeY, GraphTitle, GraphVisible, TmpFile, TmpDir).
  • Win32: WinDD 1.4.
  • Win32: new demo music by Chris Hülsbeck.
  Release 1.4.2 (03/09/2002)
   
  • Updated the Gasteiger-Marsili charge attribution.
  • GAMESS output loader.
  • Fix: mol2 sever (now the am bond order is correctly assigned).
  • Win32: PowerNet plugin: TCP/IP protocol and PDB interface.
  • Win32: the REBOL scripting language is now included in the package.
  • Win32: edit atom, residue and chain properties.
  • Win32: console command history.
  • Win32: smart move rendering option.
  • Win32: new extended commands (ChDir, ColorIdDlg, ColorRgbDlg, ConClrHist, ConCls, ConSave, ConSet, ConWin, DirDlg, ErrMsg, LogOff, MessageBox, MainWin, MiniEd, Mopac, OpenDlg, SaveDlg, SaveImg, ShutDown, SrfCalc, SrfColor, SrfColorBy, Text).
  • Win32: new system variables (ConBufSize, ConHistSize, ConPosX, ConPosY, ConSizeX, ConSizeY, ConVisible, CpuFeatures, CpuName, CpuType, CpuVendor, CurDir, GlassWin, IsRunning, Os, OsFamily, ScreenDepth, ScreenX, ScreenY).
  • Win32: TurboPack for AMD Athlon/Duron and for Intel Pentium 4.
  • Win32: new demo song by Gianna Pica.
  • Win32: updated Fmod DLL to 3.6.
  Release 1.4.1 (03/06/2002)
   
  • GAMESS cartesian file loader and saver.
  • Fix: HyperChem .hin loader.
  • Fix: XYZ detection.
  • Fix: Insight surface loader.
  • Fix: generation of solvent cluster.
  • Fix: Pentium III-M CPU detection.
  • Win32: interaction energy evaluation for the analysis of the docking results.
  • Win32: new console with direct command interface.
  • Win32: advanced cut, copy & paste routines.
  • Win32: Predator plugin interface.
  • Win32: glass windows (Windows NT/2000/XP only).
  • Win32: PLUGINGET command added.
  • Win32: Dhrystone plugin 1.1.
  • Win32: updated DevIL DLLs to 1.3.1.
  Release 1.4.0 (15/04/2002)
   
  • MDL Mol file loader.
  • Improved IFF file format (new chunks).
  • Extended command line interface for language scripting.
  • Return code handler.
  • Fix: Biosym archive 3 (.car) loader now reads the element column.
  • Fix: mol2 hack for Insight generated mol2 files.
  • Fix: mol2 saver.
  • Manual: added Frequently Asked Question (FAQ) page.
  • Win32: atom picking and interactive measures/selection (atom, distance, angle, torsion and angle betwee two planes).
  • Win32: plugin system to expand the VEGA capabilities.
  • Win32: Dhrystone Test plugin (tstdhry.dll) to test the CPU performance.
  • Win32: joystick control.
  • Win32: color requester.
  • Win32: customizable atom selection.
  • Win32: some new commands can be send trough the standard window port, in order to interpret complex command sequences.
  • Win32: now the trajectory animation is compatible with the new refresh mode.
  • Win32: the selection tool for trajectory analysis supports the atom picking. 
  • Win32: the trajectory files can be opened directly with File -> Open menu item.
  • Win32: dynamic loading for devil.dll, fmod.dll, ilu.dll, ilut.dll, libbz2.dll, z32.dll and zlib32.dll.
  • Win32: VEGA selects the DLLs with the optimizations for the installed CPU.
  • Win32: new menu items: Help -> Last error and Display -> Select -> None.
  • Win32: new demo music by Chris Hülsbeck.
  Release 1.3.2 (6/11/2001)
   
  • Now VEGA can read the DCD files in little or big endian format without conversion.
  • Added the PDB ATDL (PDBA) file support (read and write).
  • Fix: Fasta  saver.
  • Win32: more mouse controls trough the middle button and the wheel.
  • Win32: added Select menu item to show/hide a part of a molecule. 
  • Win32: added Color -> By residue, Color -> By chain and Color -> By charge menu item.
  • Win32: new Save Image output formats (Gif, Jpeg, OpenIL, PCX, PNG, PNM, Raw, SGI, Targa and Tiff).
  • Win32: added the View Settings dialog box.
  Release 1.3.1 (02/10/2001)
   
  • Win32: improved CPK visualization.
  • Win32: added VdW Dotted and Liquorice visualization modes.
  • Win32: some configuration parameters (window size and position, menu checkmarks, etc) are stored when the program is closed.
  • Win32: menu history of the opened files.
  • Win32: added window popup menu to resize the main.
  • Win32: more than one VEGA session can be opened at the same time.
  • Win32: drag & drop function to open the molecules.
  • SendVegaCmd can control more than one VEGA session.
  • SendVegaCmd asyncronous mode.
  Release 1.3.0 (13/09/2001)
   
  • Data De/Compressor Engine updated: now you can pack the output in BZip2, GZip, PowerPacker (Amiga only) and Z-Compress.
  • ILM (Molecular Hydropathicity Index) surface calculation.
  • Polar surface area calculation (PSA).
  • HyperChem HIN loader.
  • Added charge and force field check in CVFF energy evaluation.
  • Connectivity routine rewritten and more fast.
  • Surface routines totally rewritten for load/save operations.
  • DCD analyzer can load both CRD or MSF packet files.
  • Water remove option (-w) in trajectory analysis.
  • Fix: gromos loader/saver.
  • Fix: multiple PDBF loading.
  • Fix: routine for ring search.
  • Fix: CHARMm force field template.
  • Fix: a little bug in msf loader.
  • Fix: Mopac loader more compatible.
  • Fix: solvent layer calculation.
  • Linux: first official release.
  • Unix: fixed water detection routine.
  • Win32: Graphic interface with 3D OpenGL output.
  • Win32: fixed program path detection.
  • Win32: fixed CTRL+C execution halting.
  • Win32: setup program for easy insallation.
  • Win32: WinDD Data Decompressor software included in the package.
  Release 1.2
   
  • Data Decompressor Engine with BZip2, GZip, PowerPacker and Z-Compress compatibility.
  • Language localization trough the IFF catalog system and localization package.
  • Loader for Sybyl .rgn files.
  • The environment variable VEGADIR is not more needed for Amiga and Win32 versions.
  • COMFA field calculation: lypophilic.
  • CHARMm force field template fixed.
  • Biosym surface atom label fixed.
  • Amiga: fixed some endian problems.
  • Sources: multiple test script
  • Sources: Z32, Z and Bzip2 libraries and DLLs.
  • Sources: StripCR utility with patter matching
  • Win32: added pattern matching.
  • Win32: fixed msf saver.
  • Win32: fixed remove hydrogens (-r) and remove waters (-w) functions.
  Release 1.1a
   
  • Fixed an heavy bug in PDB loader and saver.
  • Mol2 filter more compatible.
  Release 1.1
   
  • First public release.
  Release 1.0
   
  • Only for internal use.