Dear Gustaf,
Thank you very much for your reply.
When I said “cannot use xleap”, I mean “command not found”.
Exactly, I run amber on the cluster using ssh -Y
rchen6.cedar.computecanada.ca <mailto:
rchen6.cedar.computecanada.ca>.
In the server, the version of amber is amber/18, however I don’t know how to check if the server has a working X-server/client installation.
As for my local computer, the mac system is version 10.13.6. I installed Xquartz version 2.7.11, Xcode version is 10.1, which is compatible with the macOS 10.13.6 system. Do I need to update both the mac system and Xcode to the newest version?
Have a nice day.
Best regards,
Rui
> On Jun 11, 2019, at 10:53 PM, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> Hello Rui
>
> First, when you say “cannot use xleap”, what exactly does that mean?
>
> Second, if you are "running AMBER on the cluster (cedar-Compute Canada)”, you are in fact not running the tutorial on a Mac, you are connecting to a Linux/Unix server from a mac using what I assume is ssh and running the tutorial on the server.
>
> Without any more information I can make some educated guesses. Assuming that the server version of amber is compiled supporting X11, that the server itself allows X-forwarding and has a working X-server/client installation. Then on your local Mac, check two things:
>
> - Have you installed XQuartz?
> - Are you connecting over ssh enabling X?
> $ ssh -Y user.serveradress
> This is important, you need to include “-Y”. Normally you would do "-X” to enable X-windows
> however this does not seem to work on newer versions of macOS and linux hosts any more.
>
> If xleap still does not work when connecting to the server, then I would guess that the problem originates server-side and you would likely have to contact the server administrators for assistance in solving the issue.
>
> Best Regards
> // Gustaf
>
> Challenging educations. Prominent research. Linnaeus University – a modern, international university in Småland, Sweden.
>
> On 12 Jun 2019, at 04:57, Rui Chen <rchen6.ualberta.ca<mailto:rchen6.ualberta.ca>> wrote:
>
> Dear sir or madam,
>
> I found a new tutorial, which used the tleap command. But before going there, I met another problem, pdb4amber command not found. Could you please help me solve the problem?
>
> Thank you,
> Rui
>
> On Jun 11, 2019, at 7:24 PM, Rui Chen <rchen6.ualberta.ca<mailto:rchen6.ualberta.ca>> wrote:
>
> Dear sir or madam,
>
> I am a new user of AMBER. I am running AMBER on the cluster (cedar-Compute Canada), following the AMBER tutorial: http://ambermd.org/tutorials/basic/tutorial0/index.htm <http://ambermd.org/tutorials/basic/tutorial0/index.htm> However, I realize this tutorial is for Linux system, I am using MacOS High Sierra, version 10.13.6. I can’t use xleap command to run LEaP, which is the first step of this tutorial. Is there a tutorial for Mac system?
>
> Looking forward to your reply.
>
> Best regards,
> Rui
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 12 2019 - 06:30:05 PDT
