Dear Gustaf,
Thank you for your help. Have a nice day.
Best regards,
Rui
> On Jun 12, 2019, at 8:07 AM, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> ‘command not found' means that the software on the server is not properly installed. This is not a problem with forwarding of GUIs, it means that there is no program called xleap in your path or it is simply not installed at all. The same is true for pdb4amber if it returns a “command not found".
>
> $ echo $AMBERHOME
>
> Should give you the path to the amber18 base directory.
>
> $ echo $PATH
>
> Prints your entire path variable.
>
> If you have no defined $AMBERHOME though everything else is properly installed, adding/defining it should solve your initial problem (command not found) and as you seem to be able to run tleap, a simple:
>
> $ which tleap
>
> Should produce the /bin folder of your amber18 base catalogue
>
> The remove everything from the end of that output up until the /amber18/ path and use the manual suggestion:
>
>
> 1. set your AMBERHOME environment variable:
>
> export AMBERHOME=/home/myname/amber18 # (for bash, zsh, ksh, etc.)
> setenv AMBERHOME /home/myname/amber18 # (for csh, tcsh)
>
>
> replacing the appropriate “/path/to/amber18” with the corresponding output from “which tleap”, removing any trailing folder name after “amber18/“.
>
> Best regards, good night and good luck.
>
> // Gustaf
>
> On 12 Jun 2019, at 15:12, Rui Chen <rchen6.ualberta.ca<mailto:rchen6.ualberta.ca>> wrote:
>
> 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> <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<mailto: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><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><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 Wed Jun 12 2019 - 09:00:03 PDT
