I was not aware that sander is now in ambertools. In fact, from present
compilation, that gave no test error,
$ which sander
/opt/amber14/bin/sander
(with my .bashrc amended as in my previous post)
Also, because of financial problems (and other reasons when remd at the
mainframe is concerned) I normally run amber from another code.
Thanks a lot for your advice.
fp
On Fri, Dec 12, 2014 at 1:43 PM, Jason Swails <jason.swails.gmail.com>
wrote:
>
> On Fri, 2014-12-12 at 12:40 +0100, Francesco Pietra wrote:
> > Hello: I compiled Linux gnu AmberTools14. However, my attempt to have
> > Amber10 also compiled (as I did before with AmberTools12) failed.
> > /opt/amber14/ambertools /opt/amber14/amber10
> >
> >
> > export AMBERHOME=/opt/amber14
> > export PATH/=$PATH\:$AMBERHOME/bin\:/opt/amber10/bin
> > export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$AMBERHOME/lib"
> >
> > I assume that Amber10 is no more compatible with. Could Amber10 be
> > separately compiled withing the /opt/amber14/amber10 or isone dropping
> into
> > a mess?
>
> A couple other points: do *not* mix source code trees. i.e. do not put
> the amber10 directory inside the amber14 directory (I'm not sure if you
> are untarring AmberTools14.tar.bz2 and then untarring Amber10.tar.bz2
> inside the amber14 directory that was created or if you are housing
> everything inside an amber14 directory you created; but it seems to be
> the former).
>
> Also, Amber 10 (and Amber 11 at this point) are not easy to compile.
> Given that sander is now part of AmberTools and the GPU version of pmemd
> only works from Amber 12 and Amber 14, there is limited advantage to
> keeping Amber 10 around... at least in my opinion.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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>
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Received on Fri Dec 12 2014 - 07:30:05 PST
