On Sat, Oct 22, 2011 at 5:38 AM, Dr. Alaa El-Din A. Abdel-Gawad <
alaael_din3.hotmail.com> wrote:
>
> Dear Jan-Philip
> Thank you for your help. I only got teleap and icon with tleap
> (non-identified, i.e. if it is a .exe or something else) and Xaleap.exe and
> I can not open it, (i.e. No universe editor). So I used teleap but for use
> antechamber when I click the icon give nothing.
>
tleap and xleap are shell scripts that properly set up your environment to
properly run teLeap and xaLeap, respectively. Again, do NOT run teLeap or
xaLeap directly, use the shell scripts instead.
I think your main problem is that you're approaching these programs as
though they're standard Windows programs that are "double-click to open".
You can't open them in an Explorer window and double-click any of the
programs, that's not how they work. You MUST use them from the
command-line. For this reason, there's a slight learning curve to using
Amber (and most other computational chemistry softwares, for that matter).
> my path is
> ~/CygwinX/home/Host/amber11/bin
> All the EXE files are in bin directory. Please, I send the log file for
> test and it seems well but I found this massage
> make: Target `test.serial' not remade because of errors.
>
That just indicates that one of the test scripts exited with an exit code !=
0, which is almost sure to happen on Cygwin if not most other platforms.
The real important part of the tests is the list of how many tests passed,
possibly failed, or exited in error. If you wanted to use functionality
that failed the tests, then you have a problem.
HTH,
Jason
>
> thank you,
>
> alaa
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Dr/Alaa El-Din A. Abdel-Gawad,
> Research Institute of Ophthalmology,
> Biophysics Unit,
> 2 Al-Ahram St.,
> 12111 Giza,
> P.O. Box: 90
> Egypt.
> e-mail: alaael_din3.hotmail.com
>
>
>
>
> > Date: Thu, 20 Oct 2011 12:51:26 +0200
> > From: jgehrcke.googlemail.com
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] AmberTools-1.5 installation
> >
> > Alaa,
> >
> > Regarding the programs you mentioned, you are supposed to run the
> > executables "tleap" and "xleap", not "teleap" and "xaleap".
> >
> > For running these executables, you need to know their path. "No such
> > file or directory" means that you've tried to execute a file that does
> > not exist.
> >
> > Do you you set the AMBERHOME environment variable? Did you compile
> > AmberTools yourself? Is $AMBERHOME/bin in your PATH?
> >
> > If you are not sure about these questions, maybe reading a basic
> > introduction to the command line and especially bash would be a good
> > idea. After a quick search, I've found these:
> >
> > http://www.tuxfiles.org/linuxhelp/shell.html
> >
> http://www.howtogeek.com/67469/the-beginners-guide-to-shell-scripting-the-basics/
> > http://vic.gedris.org/Manual-ShellIntro/1.2/ShellIntro.pdf
> >
> > Maybe a real Linux environment would make more sense in your case
> > instead of running cygwin on Windows. If you like to keep Windows as
> > your host operating system, you could think about running a real Linux
> > distribution in a virtual machine (using for example VMware Player or
> > VirtualBox).
> >
> > Best regards,
> >
> > Jan-Philip
> >
> >
> >
> > On 10/20/2011 10:40 AM, Dr. Alaa El-Din A. Abdel-Gawad wrote:
> > >
> > > Hi all
> > > yes, it is a shell program. But I imagine I sholud go through either
> teleap (terminal prompt) or xaleap (graphical interface) or antechamber and
> so on. unfortunately, although I am setting up cygwin/X, I can not go
> through Xaleap (I guess it is an Xenvironment path problem but I can't
> catch). I tried to start as follows for the tutorial 1
> > > bash: /home/Host/amber11/exe/antechamber:
> > > I got "No such file or directory"
> > >
> > > what I have do?
> > > thank you
> > >
> > > alaa
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >> Date: Tue, 18 Oct 2011 08:08:15 -0400
> > >> From: case.biomaps.rutgers.edu
> > >> To: amber.ambermd.org
> > >> Subject: Re: [AMBER] AmberTools-1.5 installation
> > >>
> > >> On Tue, Oct 18, 2011, Dr. Alaa El-Din A. Abdel-Gawad wrote:
> > >>>
> > >>> The all installed programs are in the folder called bin. When I click
> > >>> teleap I get a window for calculation. For Xeleap or sleap, I got a
> > >>> snapshot and a massage contains "open stackdump file" and the
> following
> > >>> code nimbers
> > >>>
> > >>> for antechamber, click antechamber icon recall nothing. please, what
> I
> > >>> have missed?
> > >>
> > >> You are not supposed to use the mouse to start any of these programs;
> the
> > >> codes are designed to be run from a terminal (shell), by typing the
> name of
> > >> the commands (along with other arguments) on the command line.
> > >>
> > >> ...good luck....dac
> > >>
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
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> >
> >
> > _______________________________________________
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>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Oct 22 2011 - 07:00:02 PDT
