Re: [AMBER-Developers] Experiences with sleap

From: Jodi Ann Hadden <>
Date: Sat, 5 Nov 2011 01:56:44 +0000

> 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?


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Received on Fri Nov 04 2011 - 19:00:02 PDT
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