Re: [AMBER] I have a problem in using LEaP.

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Wed, 12 Jun 2019 04:53:49 +0000

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

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Received on Tue Jun 11 2019 - 22:00:03 PDT
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