20. Frequently Asked Questions

20.1 Generic FAQ

• How is it possible to open a NAMD .coor file including atom properties ?
  The NAMD .coor file format includes only the atom coordinates. VEGA ZZ can open it but the main data of the molecule (atoms, residues, etc) are missing. To avoid this problem, you can open the file from which the .coor file was generated (usually a PDB file), thus merge the atom coordinates of .coor file by selecting File Merge in the main menu. For more information about the merge function, click here.
   

• Converting PDB into mol2 file the atom types and the bond orders are incorrect. Why ?
  If the PDB file doesn't have the hydrogens, VEGA can't detect the correct atom hybridization and the Tripos force field is assigned in wrong way.  This is not a bug and the only way to fix this problem is to add the hydrogens before the conversion.
   

• When I open some PDB files, the connectivity appears incomplete. Why ?
  Starting from VEGA 1.5.0 the PDB CONECT records are read and the connectivity isn't recalculated if the number of that record is more or equal to the number of atoms. To solve this problem, you should recalculate the connectivity for all or for the incomplete atoms, selecting Edit Add Bond from the main menu.
   

• When I try to run VEGA on my Linux RedHat 9 workstation, the message "./vega: relocation error: /usr/local/vega/liblocale.so: symbol errno, version GLIBC_2.0 not defined in file libc.so.6 with link time reference" is shown and the program doesn't start. Why ?
  This error is due to the introduction of the Native Posix Thread Library (NPTL) in Red Hat Linux 9.0. Applications complied with older Red Had distributions (e.g. VEGA and ESCHER NG) are known to experience problems with this library. To work around this problem, you can use the old Linux threads implementation by setting the environmental variable LD_ASSUME_KERNEL. Set it to either 2.2.5 or 2.4.1.
  If you are using c shell, you can enter one of the following at the LINUX prompt:
  
  setenv LD_ASSUME_KERNEL 2.4.1
  
  or
  
  setenv LD_ASSUME_KERNEL 2.2.5
  
  If you are using bash shell, you can enter one of the following at the LINUX prompt:
  
  export LD_ASSUME_KERNEL=2.4.1
  
  or
  
  export LD_ASSUME_KERNEL=2.2.5
  
  Note:
  This problem was eliminated starting from the 1.5.7 Linux release.
   

• How many atoms can manage VEGA and VEGA ZZ ?
  In theory, the maximum number of atoms manageable by VEGA is 2^32 = 4.294.967.296. VEGA ZZ can manage this number of atoms for each workspace and the maximum number of workspaces is 4.294.967.296. These numbers can't be reached by the 32 bit CPUs because their address space is 32 bit wide only.
   

• How many atoms can manage Mopac 7 included in VEGA ZZ package ?
  VEGA ZZ includes two versions of Mopac 7.01-4: Mopac_50_100.exe (max. 50 heavy atoms and max. 100 hydrogens) and Mopac_100_200.exe  (max. 100 heavy atoms and max. 200 hydrogens). The two executables are selected automatically by VEGA ZZ  for a balanced use of the hardware resources. No more than 300 atoms (100 heavy atoms + 200 hydrogens) can be used by VEGA ZZ in Mopac calculations.
   

• Can I use trajectory files and databases with 2 Gb or more sizes ?
  Yes. Starting from VEGA ZZ 2.0.2 and VEGA 1.5.3, the io64 library is linked to the executable allowing to manage files larger than 2 Gb if the file system permit it: FAT12 has a 16 Mb file size limit, FAT16 has a 2 Gb as its limit, FAT32 has 4 Gb as its limit but it's reduced to 2 Gb to allow seek operations. NTFS has a theoretical maximum file size of 16 Exabytes.
  The Linux Ext2 file system has a 4 Tb file size limit and the XFS has a  maximum file size of 16 Exabytes.
  The Amiga Fast File System (FFS) has a 4 Gb file size limit. This limit is braked by the Fast File System 2 with a theoretical maximum file size of 16 Exabytes.
   

• Why are the VEGA ZZ 2.0.6+ IFF files unreadable by previous releases ?
  The 2.0.6 release writes the IFF/RIFF files in the native little endian format (RIFF) by default. The previous releases read the IFF files in big endian format only and so they are unable to understand the RIFF files. This isn't a problem, because you can switch from little to big endian checking Big endian when you save the molecule (File Save as...). Please remember that the 64 bit IFF/RIFF files are unreadable by the previous releases.
   

• Is it available a soft or a PDF manual version ?
  No, the HTML version is available only. If you want, it's possible to build a printable version of the manual, clicking on Printable version in the left summary frame.
   

• Where could I download molecule databases ?
  Some institutions allow to access to their own databases for free. For more information click here.

20.2 VEGA ZZ FAQ

• The IFF files generated by VEGA ZZ 3.0.2+ are shown corrupted by the previous releases. Is it possible to fix the problem ?
  Due to the different visualization method implemented in the newer releases, the IFF files may be shown corrupted by previous releases. To fix the problem, just press the space bar after loading or update your VEGA ZZ installation.
   

• How can I open a trajectory file ?
  Firstly, the trajectory file must be in any format supported by VEGA ZZ (for more information, click here). Some trajectory formats need another file to be opened because they don't contain the information about atoms, residues, etc, but they include the atom coordinates only. The formats requiring an extra molecule file are: AutoDock 4 DLG, BioDock 3.0, DCD, ESCHER NG, GROMACS TRR and XTC and Quanta conformational search .csr.
  VEGA ZZ is able to find automatically the required file starting from the trajectory file name and changing the extension (e.g. my_trajectory.dcd my_trajectory.pdb). It performs changes for three times with three different file extensions (e.g. .iff, .pdb and .crd) that are typical for each trajectory format. If VEGA ZZ can't find the file, it's unable to read the trajectory. To fix the problem, two are the possible solutions:
  - Put in the same directory where is the trajectory, the molecule file with the same file name prefix of the trajectory (see the example above). VEGA ZZ can recognize if that file is compatible with the trajectory and if this condition is not satisfied, an error is shown.
  - Open the molecule file (File Open) that can be in any directory with any name, then open the trajectory file (Calculate Analysis) clicking the open button or dragging the file over the trajectory analysis window.
  For AutoDock 4 DLG, BioDock 3.0 and ESCHER NG, the associated files are obtained from the record inside the trajectory file. The AutoDock 4 DLG loader, if doesn't find  the file, performs the same procedure explained above as last chance.
   

• How is the update procedure ?
  To update the VEGA ZZ already installed in your system, you must uninstall it and thus install the new release in the same directory in which was located the previous one. No new activation is required because the vegazz.lic file isn't removed during the uninstall procedure. Starting from 3.0 release, VEGA ZZ includes an automatic procedure that checks periodically the updates. When they are available, the setups are downloaded from DDL server and installed. The user can perform manually the update selecting Help Check for update menu item.
   

• During the installation, Windows reports this error message: "Error creating registry key and so access is denied". Why ?
  The installer writes in the registry the information to uninstall VEGA. No other data are written.  The error is shown if your user account doesn't have the rights to write the registry. Logon with the administrator account and re-start the installation procedure.
   

• Why doesn't work the REBOL scripts  in my system ?
  With most probability, you installed a software firewall in your PC and so  you must configure it granting the network access to REBOL.exe. The scripting system needs the access to standard TCP/IP communication ports.
    

• Why is the REBOL script execution so slow ?
  The REBOL scripts use the TCP/IP port to communicate with VEGA ZZ. This problem affects Windows 9x and Windows 2000 only. It seems that the TCP/IP management of these OS has an excessive latency. To increase the TCP/IP performances try to use the burst commands that reduces the negotiation time. Windows XP doesn't have this problem and the scripts are executed at full speed.
     

• When I open file and load the DCD file it says "no -m option given", but no pull down menu with -m option is present. Why ?
  You opened a trajectory file directly from the File Open menu item. This procedure is incorrect for the OpenGL operating mode. The correct procedure is the following:
  - Open the whole molecule from File Open menu item.
  - Select Calculate Analysis.
  - Open the trajectory file (click on the button).
  Starting from the 1.4.0 release, you can open the trajectory file from File Open menu item. The associated molecule is loaded automatically without any request.
     

• How can I disable a plug-in ?
  You can disable a plug-in moving it to ...\Plugins\Win32\Store directory.
   

• VEGA ZZ crashes when it's showing complex molecules. How can I solve this trouble ?
  Use the OpenGL Setup utility to change the OpenGL driver from hardware to Microsoft or Mesa 3D .
   

• VEGA ZZ has low 3D performances with Matrox P-Series graphic cards when the FAA-16x anti aliasing or the stereo view is enabled. Why ?
  These graphic cards use the alpha channel to perform the aliasing reduction and the stereo view. So, if you open applications that use the alpha key, the OpenGL performances go down. A common situation is an application that uses the transparencies to make glass windows (e.g. VEGA, Miranda, WinAmp, etc). The solution is to disable the glass windows (see the control panel of the specific application) or to close the program. This problems affects Windows 2000 and not Windows XP.
   

• How can I improve the graphic quality ?
  If you have an ATI, Matrox P-series, NVIDIA graphic card, enable the anti-aliasing in the control panel of the display driver. By default, this setting is disabled. In the OpenGL mode, the Matrox driver supports the 16x anti-aliasing only.
  Enable the vector anti-aliasing in the VEGA ZZ View settings window.
   

• How does VEGA add the solvent molecules ?
  VEGA uses a pre-calculated solvent cluster placed in ...\VEGA ZZ\Data\Clusters directory that is a PDB gzipped file. When you add solvent clusters to a solute, VEGA performs these steps:
  
  - load the solvent cluster;
  - move the solute at the centre of the cluster (it have a cubic shape);
  - cut the volume occupied by the solute removing the bumping molecules;
  - cut the shape as you selected in the graphic interface (box, sphere, layer).
  
  When you choose Sphere, VEGA cuts a sphere of specified radius cantered at the barycentre of the solute. When you select Layer, it cuts the molecules exceeding the distance between them and the closest atom on the surface. Choosing the Box mode, VEGA cuts the solvent molecules outside the box user-defined dimensions. The box is cantered at the barycentre of the solute as for the sphere mode.
  This is a generic method for all kinds of solvents. The direction of the water h-bonds referenced to the solute is not taken in account. For this reason, after the solvation, you must optimize the system performing an energy minimization and, eventually, a short molecular dynamics.

20.3 VEGA ZZ activation problems.

• I didn't received the Activation Key because I inserted a wrong e-mail address in the registration form. How can I change it in order to activate the software ?
  The procedure is very easy:
  - Connect to DDL license server: http://www.ddl.unimi.it/licman/login.htm.
  - Login with the wrong e-mail address and the password specified during the registration procedure.
  - In the menu, select Update user details and click Go !
  - Change the e-mail address and click Update.
  - Repeat the activation procedure with the new e-mail address.
  - A warning message will be shown, informing you that the Product Key is already active.
  - Request a copy of the Activation Key that will be sent to you at the new e-mail address.
   

• My Activation Key is lost. Can I request a copy ?
  Yes ! Repeat the activation procedure: a warning message informs you that your Product Key is already active. Request a copy of it clicking the link.
   

• I have several PCs and I would like to install VEGA ZZ on all of them. Can I obtain more than one Activation Key ?
  Yes ! There are no limits in the number of activations. Please use the same e-mail address for all activations to avoid to compile the registration form each time.
   

• My Activation Key is expired. How can I obtain a new one ?
  Repeat the activation procedure and replace the vegazz.lic file with the new one sent to you by the activation server.
   

• I received the e-mail with the Activation Key but I'm unable to open it. Why ?
  The Activation Key is a encrypted binary file and VEGA ZZ only is capable to decrypt and read it. You must follow the activation procedure reported in the e-mail and in the activation wizard: you must save the vegazz.lic file in the Data folder placed in the installation directory. Starting from the 2.0.8 release, if you try to open the vegazz.lic file, it's automatically copied in the installation directory and if it's already present, a warning message is shown.
   

• When I try to install the Activation Key, the invalid license file name message is shown. How can I fix this problem ?
  With most probability, you changed the the activation file name from vegazz.lic to another one or you tried to open it directly from the e-mail client that decodes it, creating a temporary file that isn't named correctly.
  Try to save the file and double click on it.
  Another common problem is due to Windows default setting, hiding the extension of known files. In particular, if you rename the activation key to vegazz.lic, the OS keeps the previous .lic extension making the real file name as vegazz.lic.lic even if vegazz.lic file name is shown. There are two possible solutions: 1) remove the .lic file extension; 2) go to the file explorer settings (Folder options window -> View tab -> Advanced settings list) and uncheck Hide extensions for known file types.
   

• VEGA ZZ says to me that my system has an invalid host ID or a CRC error is present in my Key. Few days ago, the software worked fine. Why ?
  Your host ID is changed and this is possible when the hardware network configuration is changed adding a new network card, modem, IEEE 1394 card etc or updating the motherboard BIOS and/or device drivers. In this situation, the solution is repeat the activation procedure.
   

• It's possible to create an Activation Key for a computer not connected to Internet ?
  Yes, it's possible following this procedure:
   
  NC is the PC not connected to Internet.
  C is the PC connected to Internet.

1. Download VEGA ZZ with C.
2. Transfer the package from C to NC (e.g. by pen drive, CD, etc).
3. Install the package on NC and start VEGA ZZ. The activation wizard will be show.
4. Annotate the Product Key. Please remember that it's not the same of C.
5. Start Internet Explorer in C and connect to http://www.ddl.unimi.it/licman.
6. Put the Product Key of NC, your e-mail address and complete the activation as usual.
7. When you receive the e-mail with the vegazz.lic file, transfer it to NC and copy it un the ...\VEGA ZZ\Data directory. VEGA ZZ on NC is now operative.