Re: [AMBER-Developers] Experiences with sleap

From: Yong Duan <>
Date: Fri, 04 Nov 2011 20:57:23 -0700

I second this.

I believe we now have two different approaches to get SCNB/SCEE into
prmtop using tleap. I am sure we will be able to consolidate and unify.


On 11/4/11 6:56 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 res!
> t of us have?
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Received on Fri Nov 04 2011 - 21:00:04 PDT
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