AMBER Archive (2008)

Subject: Re: AMBER: xleap and Sirius on ubuntu 8.04

From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Thu Sep 11 2008 - 22:22:38 CDT

Taufik,
Regarding the Sirius issue, it looks like it's a video card problem,
since you have just the basic integrated graphics. Sirius typically
requires somewhat better hardware for optimal performance (a dedicated
graphics card). It doesn't need to be fancy, just something with maybe
32MB of dedicated video memory.. Have you tried loading these molecules
on a different computer, perhaps with a better graphics?
Also, what specifically are you trying to load?

Sasha

alsarraj wrote:
> Hello,
> I recently switched to Ubuntu from irix, I compiled AmberTools 1.2
> xleap seems to work with few problems i cannot select File, Edit or
> Verbosity using the mouse. However i can type the commands just fine. I
> can load a molecule and edit it but i cannot use the Unit Edit or
> Display menu. They are visible and i can see the functions under each
> header but i cannot select any of the functions like check unit or
> calculate net charge. Could this be a video card problem? i think i have
> the correct drivers installed.
>
>
> When loading one molecule with Sirius things seem to work well, once a
> load a second molecule (i want to connect two molecules together) both
> disappear and after clicking on the empty screen one would flicker on
> screen while one will not appear at all. I have been able to -and still
> can- use xleap on my irix machine. I have not used Sirius on Irix.
>
> below is my lspci output
> "taufik_at_taufik-desktop:~/Project/April/Linker$ lspci
> 00:00.0 Host bridge: Intel Corporation 82865G/PE/P DRAM
> Controller/Host-Hub Interface (rev 02)
> 00:02.0 VGA compatible controller: Intel Corporation 82865G Integrated
> Graphics Controller (rev 02)
> 00:1d.0 USB Controller: Intel Corporation 82801EB/ER (ICH5/ICH5R) USB
> UHCI Controller #1 (rev 02)
> 00:1d.1 USB Controller: Intel Corporation 82801EB/ER (ICH5/ICH5R) USB
> UHCI Controller #2 (rev 02)
> 00:1d.2 USB Controller: Intel Corporation 82801EB/ER (ICH5/ICH5R) USB
> UHCI Controller #3 (rev 02)
> 00:1d.7 USB Controller: Intel Corporation 82801EB/ER (ICH5/ICH5R) USB2
> EHCI Controller (rev 02)
> 00:1e.0 PCI bridge: Intel Corporation 82801 PCI Bridge (rev c2)
> 00:1f.0 ISA bridge: Intel Corporation 82801EB/ER (ICH5/ICH5R) LPC
> Interface Bridge (rev 02)
> 00:1f.1 IDE interface: Intel Corporation 82801EB/ER (ICH5/ICH5R) IDE
> Controller (rev 02)
> 00:1f.2 IDE interface: Intel Corporation 82801EB (ICH5) SATA Controller
> (rev 02)
> 00:1f.3 SMBus: Intel Corporation 82801EB/ER (ICH5/ICH5R) SMBus
> Controller (rev 02)
> 00:1f.5 Multimedia audio controller: Intel Corporation 82801EB/ER
> (ICH5/ICH5R) AC'97 Audio Controller (rev 02)
> 05:02.0 Ethernet controller: Broadcom Corporation NetXtreme BCM5782
> Gigabit Ethernet (rev 03)"
>
> Thank you,
> Taufik
>
>
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