AMBER Archive (2009)

Subject: Re: [AMBER] xleap-does not work

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Sun Oct 11 2009 - 06:01:07 CDT

Dear Dr. Jason,

Thanks for your kind remind. With the help from Case, my problem on xleap has been solved.
Best Regards,

Rilei Yu

--- 09年10月11日，周日, Jason Swails <jason.swails_at_gmail.com> 写道：

发件人: Jason Swails <jason.swails_at_gmail.com>
主题: Re: [AMBER] xleap-does not work
收件人: "AMBER Mailing List" <amber_at_ambermd.org>
日期: 2009年10月11日,周日,上午1:08

Rilei,
I think your problem is rooted in ubuntu rather than xleap.  Which version
of ubuntu are you using?

Versions 8.10 through 9.04 never came with the necessary x libraries
installed, so xleap could not be installed
without first installing the proper xlibs from aptitude.  My solution
to that was to install every instance of x-libraries available through
apt-get, after which I was able to compile and run xleap.  However, I
believe that there is either a conflict amongst some of the libraries I
installed, or the ones xleap is looking for are just a little bit different,
and none of the buttons in the pull-down menu work (I don't remember if I
had this problem in version 8.04 LTS).  I've never had this problem with any
other platform I used, including Mac OS X and even Cygwin awhile ago, and I
also cannot remember exactly which package(s) allowed me to compile xleap,
since I more often use the text-based tleap and sleap.  Moreover, tracking
down the culprit x11 library responsible for these bugs appeared to be too
daunting a task for the returns, so I never attempted it.  (Especially since
I had working versions of xleap on my other machines running different
operating systems).  Are these the problems you're having?

As user-friendly as Ubuntu is for regular linux use, the installation CDs
are painfully sparse as far as the software they bundle in the CD.  Many
packages that come as default in SUSE or Fedora are omitted in Ubuntu (I
believe so they can keep the size of the image to the CD level rather than
jumping up to DVDs like the other distributions have done).

All the best,
Jason

On Sat, Oct 10, 2009 at 9:53 AM, case <case_at_biomaps.rutgers.edu> wrote:

> On Sat, Oct 10, 2009, Rilei Yu wrote:
> >
> > it seems that I have been obsolete, I always
> > thought there should be not change in amber10 and amber9 in such basic
> > operation. Before, when I used amber9, these force parameters were
> > loaded automatically.
>
> I suspect you are mis-remembering what happened.  The last version of Amber
> to
> have a "default" force field was Amber 6.
>
>
> > After I load the force field one by one using
> > source, the protein can be load without complain. But another problem is
> > still cannot be solved:
> > I open a window, using "edit a"
> > then I chose several atoms and want to edit them in the window. However,
> > when I chose "edit" on the top of the window, and click "edit selected
> > atoms", there was no response.
>
> I can't reproduce this problem.  My only guess is to check the NumLock and
> CapsLock status:
>
>   http://ambermd.org/Questions/xleap.html
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

      ___________________________________________________________ 
  好玩贺卡等你发，邮箱贺卡全新上线！ 
http://card.mail.cn.yahoo.com/
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber