Re: [AMBER-Developers] Experiences with sleap

From: Wei Zhang <>
Date: Fri, 4 Nov 2011 21:17:32 -0500

On Fri, Nov 4, 2011 at 8:56 PM, Jodi Ann Hadden <> wrote:

> > so this time some initial features should be ones not in tleap to
> > guarantee a user base.
> Must be careful here... New features not available in tleap is how sleap
> got it's user base -- the GLYCAM lab, who as of AMBER 11 were forced to use
> sleap in order to simulate carbohydrates with the correct SCEE/SCNB values.
> As someone whose research suffered severely from that fiasco, I make the
> request that before something is done that "forces" users to switch to the
> new leap that this leap at least support all the functionality supported by
> tleap and build things at least as correctly as tleap does. The output of
> this new leap must be rigorously checked against the output of tleap (if
> what comes out of tleap is what we are taking to be the correct answer), or
> there must otherwise be some method for ensuring the output is sane and
> what was expected for the structure. I always found that to be the most
> tragic feature of sleap -- the basic inability to compare/cross-check sleap
> prmtops with trusted tleap ones. If the sleap devs weren't even doing that,
> what hope did the rest of us have?

exactly, if we are going to rewrite, we need to guarantee the exact same
output as tleap.

> Jodi
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Received on Fri Nov 04 2011 - 19:30:02 PDT
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