On Fri, 2014-03-14 at 13:37 -0400, Wook Lee wrote:
> Dear Jason
>
> Thank you for your reply.
> I only have AMBER 11, so I want to install Ambertools 1.5.
> (As far as I found in the internet, even if I want to use Ambertools 12
> or 13 with AMBER 11,
> I need to install Ambertools 1.5 first.)
>
> As for you suggestion, all the installations I tried, they all started
> from scratch.
> I also have been to your website and followed the instruction there,
> but I still had those errors.
> Is there any way to solve this problem?
So I tried it out in a virtual machine and saw the problems you
mentioned. By default, SUSE does not come with readline installed, so
the Python interpreter that AmberTools 1.5 builds is broken. You need
-nopython to get around that, as you saw.
Also, SUSE automatically builds the NetCDF libraries to
$AMBERHOME/AmberTools/lib64, yet the Amber build script looks for them
in $AMBERHOME/lib. So what you have to do is make sure that all
libraries that are in $AMBERHOME/AmberTools/lib and
$AMBERHOME/AmberTools/lib64 are moved to $AMBERHOME/lib, and all
libraries installed to $AMBERHOME/lib64 are moved to $AMBERHOME/lib as
well. Then, you need to make sure that $AMBERHOME/lib64,
$AMBERHOME/AmberTools/lib, and $AMBERHOME/AmberTools/lib64 are all
symlinks to $AMBERHOME/lib.
After I did that, the build finishes. So "is there any way to solve the
problem?" -- yes. But just like any outdated code it's very much a
"play around until it works" type of thing (try installing Python 1.5,
for instance...) AmberTools 1.5 really is no longer supported (nor is
Amber11 for that matter), so for the most part you're on your own.
HTH,
Jason
P.S. The commands below should implement the sequence of tasks I
detailed above. They're untested, so go over them before
copying-and-pasting.
cd $AMBERHOME
mv AmberTools/lib/* lib
mv AmberTools/lib64/* lib
rm -fr AmberTools/{lib,lib64}
mv lib64/* lib
rmdir lib64
ln -s lib lib64
cd AmberTools
ln -s ../lib
ln -s ../lib lib64
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Mar 14 2014 - 12:30:02 PDT
