Dear All,
I used bash sell to start the Amber Tutorial B1 section-2 but I get the the following massage
Host.usr $ $AMBERHOME/exe/ncgen -o -i nuc.in -o nuc.out -d $AMBERHOME/dat/leap/parm/ncgen.dat nuc.pdb
ncgen: -: ncgen: only one input file argument permitted
thank you
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: Sat, 22 Oct 2011 09:41:02 -0400
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] AmberTools-1.5 installation
>
> 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
> > > >>
> > > >>
> > > >> _______________________________________________
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> > > >> http://lists.ambermd.org/mailman/listinfo/amber
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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 Sun Oct 23 2011 - 02:00:02 PDT
