From: andrea spitaleri (
Date: Wed Apr 19 2006 - 05:37:23 CDT

Hi all,
the contact map plugin under analysis menu may analyze the contact between ligand and protein?
In first instance, it doesn't. Any t&t?



Marc Petitmermet wrote:
> On 18. Apr 2006, at 13:13 Uhr, Marc Petitmermet wrote:
>> I have this strange error upon starting vmd 1.8.4 (or 1.8.4b11) and
>> fully patched Fedora Core 5:
>> Tk startup error: this isn't a Tk applicationunkown color name "Black"
>> Could not read the vmd initialization file -
>> source {/usr/local/lib/vmd/scripts/vmd/vmdinit.tcl}
>> can't invoke "wm" command: application has been destroyed
>> The VMDDIR environment variable is set by the startup
>> script and should point to the top of the VMD hierarchy.
>> VMD will continue with limited functionality.
>> invlid command name "vmd_load_extension_packages"
>> I did not have this problem with test 3 of Fedora Core 5 and the
>> vmd-1.8.4b11. Something must have been changed. I used the standard
>> installation procedures (unpack; ./configure; cd src; make install);
>> vmd files from earlier installations, if any, were removed before the
>> installation. FC5 contains tk-8.4.12-1.2 and tcl-8.4.12.-4.
>> When starting /usr/local/lib/vmd/vmd_LINUX I get first the error:
>> Tcl startup error: Can't find a usable init.tcl in the following
>> directories:
>> (here comed a list of directories that do not exist in FC5)
>> and then the same error message as mentioned before.
>> How can I fix this problem? Am I missing something in my installation?
> Ok. My mistake. Had a nonexistent RgbPath setting in xorg.conf. Just
> removed it and the problems are gone.
> Regards,
> Marc

Andrea Spitaleri
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
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