AMBER Archive (2007)

Subject: Re: AMBER: Cygwin error

From: Lili Peng (lilipeng_at_gmail.com)
Date: Thu Aug 09 2007 - 14:16:20 CDT

I'm running the command from startwinx.bat of Cygwin (it provides a
graphical interface).

On 8/9/07, Gustavo Seabra <gustavo.seabra_at_gmail.com> wrote:
>
> Are you trying this command from a xterm in cygwin? or from the cygwin
> bash prompt?
> Gustavo.
>
> On 8/9/07, Lili Peng <lilipeng_at_gmail.com> wrote:
> > Dear all,
> >
> > Thanks all for your helpful comments. I've installed the tcsh package
> in
> > Cygwin. However, I've encountered another problem. When I try to run
> xleap
> > by typing "$AMBERHOME/exe/xleap -s -f
> > $AMBERHOME/dat/leap/cmd/leaprc.ff99SB" I just end up
> > getting the following message:
> >
> > "/cygdrive/h/amber9/exe/xaLeap: /cygdrive/h/amber9/exe/xaLeap: cannot
> > execute binary file"
> >
> > I've also tried the following:
> > $ xleap
> > /cygdrive/h/amber9/exe/xaLeap: /cygdrive/h/amber9/exe/xaLeap: cannot
> execute
> > binary file
> >
> > $ xaLeap
> > ./xaLeap: ./xaLeap: cannot execute binary file
> >
> > I wondered whether it was a permissions problem, so I tried:
> > $ ls -ll xaLeap
> > -rwx------+ 1 Lili None 3467265 Mar 29 15:54 xaLeap
> >
> > ...Obviously I have read, write, and execute access, so it can't be a
> > permissions issue..
> >
> > Does anyone have insights on the problem?
> >
> > Thanks,
> > Lili
> >
> >
> > On 8/8/07, Gustavo Seabra <gustavo.seabra_at_gmail.com > wrote:
> > >
> > > On 8/8/07, Lili Peng <lilipeng_at_gmail.com > wrote:
> > > > I think I figured it out. I have to run:
> > > >
> > > > cd "$AMBERHOME"
> > > > or
> > > > ls "$AMBERHOME"
> > > >
> > > > cd or ls don't work without the quotes.
> > >
> > > That's weird, it works fine for me. Which shell are you using? The
> > > default in cygwin in bash, which is the one I use, and just "cd
> > > $AMBERHOME" works just fine.
> > >
> > > > Still, this doesn't solve the problem with running xleap, but I
> think
> > that's
> > > > a problem with csh. I didn't have it installed, so now I'm going
> back
> > into
> > > > the Cygwin setup file and installing the csh file.
> > >
> > > Well, that's another thing. This is unrelated to the error you
> > > reported before, but yes, you need csh. In Cygwin, "csh" is actually a
> > > symlink to "tcsh":
> > >
> > > $ which csh
> > > /usr/bin/csh
> > > $ ls -l /usr/bin/csh
> > > lrwxrwxrwx 1 adm None 8 Jun 7 15:47 /usr/bin/csh -> tcsh.exe
> > >
> > > The problem is that tcsh is not installed by default. You need to run
> > > setup.exe again and explicitly select it from the "shells" menu. The
> > > link from csh is created automatically.
> > >
> > > Gustavo.
> > >
> > -----------------------------------------------------------------------
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> > >
> >
> >
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