On Thu, Mar 24, 2016 at 9:27 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> I installed ambertools 1.5 on OSX to avoid doing my taxes. Thanks to an
> OSX upgrade, my delaying tactic was effective - who would have thought
> I'd need to uninstall/rebuild/reinstall all my ports just to get
> gfortran, and that I'd have to fix two broken upgrade steps, and
> research/hack a lib soft link to restore gimp happiness along the way?
> Why should the registry be locked when building a package? Nice to see
> the osx UI still functions ok while CPU pegged building things, at least.
>
> Here are notes on the Amber part of the install, which went smoothly
> (writing as the creator of the first Amber release package that wasn't a
> copy of the shared source tree on a DEC VMS machine). Aside from my
> xleap problem, my only complaint is that I had to install fortran when I
> don't expect to use any fortran progs.
>
> -- http://ambermd.org/AmberTools15-get.html
>
> It would be nice to quote the appropriate tar command on this page,
> since I haven't dealt with a .tar.bz2 file before. Admittedly 'tar tf
> AmberTools15.tar.bz2' just works on OSX, but still, I took some time to
> search for the right command.
>
tar jxvf AmberTools15.tar.bz2
> -- extracted dir is amber14, not amber15
This is to ensure interoperability with Amber 14. We've never really
figured out a good way around this that was simultaneously simple and not
prone to common errors.
> README also says amber14, including license claim.
>
> -- configure gnu
>
> It would be nice if there was an option to skip the fortran programs.
>
I doubt this is likely to happen. "Skipping the Fortran programs" would
leave only a few components behind, since nothing that depended on any
Fortran libraries (blas, lapack, etc.) could be built. So no cpptraj,
sander, sqm, pbsa, NAB, RISM, antechamber, MM/PBSA, pmemd, pmemd.cuda,
etc. You'd be left effectively with leap, parmchk, ParmEd, and (if you
*really* wanted it) a hobbled cpptraj. It's a mode few users would use and
(almost) no developers would test. Add in the required effort to make this
a reality, and it's just not a sensible way to spend limited developer
time.
As an aside, there's a much easier way to install gfortran.
https://gcc.gnu.org/wiki/GFortranBinaries#MacOS with instructions here:
https://gcc.gnu.org/wiki/GFortranBinariesMacOS
It doesn't install gcc or g++, but you can just use
./configure -macAccelerate clang
to use the system C and C++ compilers instead (but you still need gfortran).
-- xleap
>
> Edit: couldn't deselect selected atoms. Would be nice to have popup help
> for the edit window controls, and an Edit dropdown cmd to deselect when
> there is os-specific breakage of these instructions: " If you played
> with selecting atoms using the left mouse button you can deselect a
> region by holding down the/Shift/key while drawing the selection
> rectangle. To select everything, double click the LEFT button (and to
> deselect, do the same while holding down the/Shift/key)."
> http://ambermd.org/tutorials/basic/tutorial1/section2.htm and similar
> http://ambermd.org/tutorials/advanced/tutorial1/section3.htm
You can also type "deselect <unit>" in the text console. The GUI toolkit
used in xleap is pretty archaic, and I don't think many people (anybody?)
knows enough to do this kind of thing. The UI could definitely use work
(probably overhaul or plug it into an existing modeler that is more
feature-complete)... just a question of available developer hours.
Next best thing... put it in the tutorials :).
All the best,
Jason
--
Jason M. Swails
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Received on Fri Mar 25 2016 - 09:30:06 PDT
