Re: [AMBER-Developers] amberlite and GIT

From: Jason Swails <>
Date: Fri, 13 Mar 2015 17:19:02 -0400

On Fri, Mar 13, 2015 at 5:08 PM, Daniel Roe <> wrote:

> Hi All,
> Maybe I'm the only one who was suffering from this, but just in case
> not I figured I'd send this around.
> I have noticed that sometimes when I configure/compile inside a GIT
> tree, files from amberlite end up changed, e.g.
> # modified: ../AmberTools/src/amberlite/pdb4amber05/pdb4amber
> # modified: ../AmberTools/src/amberlite/pymdpbsa
> # modified: ../AmberTools/src/amberlite/pytleap
> Usually in the past I have just done 'git checkout' and not bothered
> to look into it. However I'm currently compiling Amber at least 10
> times a day in various places lately and this started to tilt me.
> Looking into it further, it appears that at some point in the past
> symlinks were created from these files into $AMBERHOME/bin. Then at
> some point later the amberlite setup process changed to something like
> this:
> sed -e "s.PYTHONEXE.$PYTHON.g" < pymdpbsa > $AMBERHOME/bin/
> Problem is of course that if those previous symlinks are still hanging
> around the files end up overwriting themselves. Remove the symlinks
> and the problem is solved.

‚ÄčAre they still symlinks?

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER-Developers mailing list
Received on Fri Mar 13 2015 - 14:30:05 PDT
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