Re: [AMBER-Developers] Experiences with sleap

From: Scott Brozell <>
Date: Fri, 4 Nov 2011 20:47:10 -0400


On Thu, Nov 03, 2011 at 02:45:44PM -0700, Ross Walker wrote:
> Look at the example we have here. We have a working code, tleap / xleap that
> had some problems and needed some extra stuff adding etc. But instead of
> people trying to fix stuff we get a whole new version written from scratch
> which has its own problems. Why oh why are we making yet another imperfect
> square wheel?

Your analysis is not on the mark:
First there was fixing of tleap; i know since i did some of it.

Second, my opinion as a professional computer programmer was and is that
tleap needed to be thrown away and rewritten. [ tleap was a great
success, but much better software development tools have come along. ]

Third, the sleap rewrite used a far too generic tool/approach IMHO;
the main problem with tleap is that there is a lot of code to do
things that are non-trivial in C but are simple in C++;
the main problem with sleap is that there is a lot of code to do
things in a far too generic way; a focused C++ rewrite based on
the STL could produce a far better product than either tleap or sleap.

Fourth -- on what to do now -- throw them both away; rewrite tleap in
C++ using the STL by starting small and proceeding incrementally.
We have the talent to do this. The apparently agreed upon failure
of sleap was a failure of the Amber development community. sleap
didn't get used soon enough; leadership, ie Dave, did say to use;
so this time some initial features should be ones not in tleap to
guarantee a user base. We may have a kernel of the aleap (Amber LEaP)
in cpptraj, maybe we can start there. Once the ball is rolling we can
rework parts from tleap/sleap. Go team go :)


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Received on Fri Nov 04 2011 - 18:00:02 PDT
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