[AMBER-Developers] amberlite and GIT

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Fri, 13 Mar 2015 15:08:50 -0600

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

 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.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Mar 13 2015 - 14:30:04 PDT
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