Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16

From: Bill Ross <ross.cgl.ucsf.edu>
Date: Sun, 04 Sep 2016 17:53:08 -0700

Have you tried rebooting?
Bill

<div>-------- Original message --------</div><div>From: sunyeping <sunyeping.aliyun.com> </div><div>Date:09/04/2016 4:30 PM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org>, "david.case" <david.case.rutgers.edu> </div><div>Subject: Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 </div><div>
</div>Hi, Thank you and Bill for your reply. Hoping you are correct. But can you help me with this Internet conneting problem? I cannot work properly with it without internet connecting.
My OS is Centos 6.7, and the version of Network manager is Applet 0.8.1. When clinking the Network manager icon at the upper right conner at the Desktop of my compuer, I can see in the pop-up manu that there are two network cards (Intel 82573E Gigabit Ethernet Controller (Copper) and Intel 82573L Gigabit Ethernet Controller) but only one link (System eth1) available. Usually when clicking the "System eth1" the Internet connection would be established. However from the last morning clicking the "System eth1" only gives connect "nectwork connectiong has been disconnected" information.
   But when I give "ifconfig" command in a gnome terminal, the output information seems to be correct:

[sunyp.localhost Desktop]$ ifconfig
eth0 Link encap:Ethernet HWaddr 00:25:90:72:E2:86
          UP BROADCAST MULTICAST MTU:1500 Metric:1
          RX packets:0 errors:0 dropped:0 overruns:0 frame:0
          TX packets:0 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:0 (0.0 b) TX bytes:0 (0.0 b)
          Interrupt:16 Memory:faee0000-faf00000

eth1 Link encap:Ethernet HWaddr 00:25:90:72:E2:87
          inet6 addr: fe80::225:90ff:fe72:e287/64 Scope:Link
          UP BROADCAST RUNNING MULTICAST MTU:1500 Metric:1
          RX packets:49 errors:0 dropped:0 overruns:0 frame:0
          TX packets:11 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:16386 (16.0 KiB) TX bytes:3038 (2.9 KiB)
          Interrupt:17 Memory:fafe0000-fb000000

lo Link encap:Local Loopback
          inet addr:127.0.0.1 Mask:255.0.0.0
          inet6 addr: ::1/128 Scope:Host
          UP LOOPBACK RUNNING MTU:65536 Metric:1
          RX packets:90 errors:0 dropped:0 overruns:0 frame:0
          TX packets:90 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:0
          RX bytes:6737 (6.5 KiB) TX bytes:6737 (6.5 KiB)
And When I pass "nm-applet" command in a terminal, it returns:
 [root.localhost Desktop]# nm-applet

** (nm-applet:7709): WARNING **: <WARN> bus_init(): Could not get the session bus. Make sure the message bus daemon is running! Message: Did not receive a reply. Possible causes include: the remote application did not send a reply, the message bus security policy blocked the reply, the reply timeout expired, or the network connection was broken.

GConf Error: Failed to contact configuration server; some possible causes are that you need to enable TCP/IP networking for ORBit, or you have stale NFS locks due to a system crash. See http://projects.gnome.org/gconf/ for information. (Details - 1: Failed to get connection to session: Did not receive a reply. Possible causes include: the remote application did not send a reply, the message bus security policy blocked the reply, the reply timeout expired, or the network connection was broken.)
An instance of nm-applet is already running.

(nm-applet:7709): GConf-WARNING **: Directory `/system/networking/connections' was not being monitored by GConfClient 0xaf1920

So could you help me solve the problem?
Best regards.
Yeping------------------------------------------------------------------From:David A Case <david.case.rutgers.edu>Time:2016 Sep 5 (Mon) 06:01To:孙业平 <sunyeping.aliyun.com>; AMBER Mailing List <amber.ambermd.org>Subject:Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16
On Sun, Sep 04, 2016, sunyeping wrote:

> I stalled ambertool 16 yesterday in my computer. The OS in my compter
> is CenOS6.7. The install seemed to be very successful and "make test"
> gives only two failure. Unfortunately when I started my compter today, I
> find the NetWork Manager in my system cannot connet to the Internet. Did
> it cause by certain change in the system when intalling the ambertool
> 16? Do you also encounter some a problem? How can I do now?

The amber install procedure changes only files in the $AMBERHOME directory
tree. As Bill noted, it does nothing that could affect internet connectivity.

....dac
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Received on Sun Sep 04 2016 - 18:00:02 PDT
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