Re: AMBER: Cygwin error

From: Lili Peng <>
Date: Thu, 9 Aug 2007 11:13:27 -0700

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?


On 8/8/07, Gustavo Seabra <> wrote:
> On 8/8/07, Lili Peng <> 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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Received on Sun Aug 12 2007 - 06:07:38 PDT
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