7. Frequently Asked Questions
7.1 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.
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 showed 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
7.2 OpenGL FAQ
When VEGA OpenGL starts, the error message
"This program has performed an illegal operation and will be shut down. If the
problem persists, contact the program vendor" (module I81XGICD.DLL). Why ?
The ICD driver of Intel 81x chipsets (810E, 810E2, 810EP, 815, 815E, 815E2 and
815EP, 845) is buggy and isn't compatible with VEGA releases before the
1.5.0. The ways to solve this problem are:
1. download the latest VEGA release that include a patch for these graphic
chips;
2. from the control panel set the number of color to 256;
3. try to download the old OpenGL32.dll
and copy it in the VEGA installation directory;
4. buy a cheap AGP graphic card (impossible with Intel 810 chipsets).
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.
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 don't include BioDock 3.0 that will be available as soon as possible.
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 ?
download the old OpenGL32.dll
and copy it in the VEGA installation directory. This problem was found with
SiS 315 GPU and Windows 2000 SP-3.