19. Frequently Asked Questions
19.1 Generic FAQ
How can I obtain the full release to
calculate the Virtual logP ?
The Virtual logP and MLP calculations are possible only in the VEGA full version that
is compiled with the routines copyrighted by Bernard Testa. You must buy the CLIP package
from Bernard Testa in order to obtain the regular license to use them. Only in this case,
I can send to you the full VEGA version (that is free like as the standard). For more
information, see: http://www-ict.unil.ch/ict/clip/docs/main_clip.html.
VEGA ZZ includes the Virtual logP calculation capability.
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 solve this problem is adding all hydrogens.
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
How many atoms can manage VEGA and
VEGA ZZ ?
Theorically, 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 de 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.
19.2 VEGA ZZ FAQ
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.
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 operating system is Windows NT 4/2000/XP and
your user account doesn't have the rights to write in the registry. Please 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.
VEGA doesn't save the preferences when it
exits or I can't edit the template files. Why ?
Your operating system is Windows NT 4/2000/XP and your user account doesn't have the
rights to write in the Data directory. Please logon with the
administrator
account and change the permissions of the Data directory to everyone/full control.
This problem is solved in the 1.5.1 release that sets automatically the
permissions during the setup procedure.
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.
Why doesn't work the docking module
(BioDock) ?
VEGA includes the graphic interface for the BioDock docking software. The standard VEGA
package doesn't include BioDock 3.0.
Can I disable the glass windows ?
Select
Tools -> Edit prefs from the main menu, find the keyword GLASSWINDOWS,
change the value from 1 to 0 and save the settings (File -> Save). Restart
VEGA and the glass windows will be disabled (see prefs file
specifications).
How can I disable a plug-in ?
You can disable a plug-in moving it into the \Plugins\Store directory.
VEGA crashes when it shows
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 the
system with Windows 2000 and not with 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.
19.3 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.
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.