AMBER Archive (2008)

Subject: AMBER: xleap and Sirius on ubuntu 8.04

From: alsarraj (
Date: Thu Sep 11 2008 - 21:45:54 CDT

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,

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