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.
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.
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
> >>
> >>
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
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>
>
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- application/octet-stream attachment: tleap.doc
Received on Sat Oct 22 2011 - 03:00:03 PDT
