Re: [AMBER-Developers] AT Manual feedback request

From: Jason Swails <>
Date: Sun, 27 Nov 2011 00:06:48 -0500

On Nov 26, 2011, at 11:43 PM, B. Lachele Foley wrote:

> I will alter the manual a little more to address Dave's statements/questions and tell you when I'm done. I do appreciate the comments.
> I don't come from a biochem background at all, so it would be interesting for the manual to say something about "psi in residue 2" -- in this interdisciplinary field, it helps to know that biochem folks think about it that way. To me, those torsions are a property of the combination of the two residues, but I can see the efficiency in considering them to be a property of only one. It isn't so simple for sugars, tho one can consider a set of torsions as being "owned" by the residue containing the anomeric center. Anyhow -- I presume this is one of the chemical assumptions Dave spoke of.
> I recommend against changing the functioning of the impose command at this point unless you truly believe it to be incorrect behavior. Whatever it does, it's done it for a long time, and folks are used to it. I'll just make sure the manual explains it. However, I'd be all for some additions like set torsion, set angle & set distance that will set internals. It would also be nice if they didn't require serially bonded atoms, though I can see difficulty deciding which atoms move. A ptraj-like syntax would be fine, but using the typical leap-like syntax would work, too. I'm thinking something like {m.3.C2 m.3.C1 m.2.O4 m.2.C4}. We're going to use that syntax in our builder to keep it as consistent with leap as possible, tho we might support the other mask as well at some point.

I strongly agree here with Lachele. I'm all for extending leap and making it bigger and better than ever. However, I _don't_ think we should mess with any existing commands at all unless absolutely necessary, especially until we get a comprehensive test suite in place. We can add new functionality, but the existing functionality has been around for so long that messing with it will surely bring only pain and frustration (and we need to add tests for those functionalities to make sure we're not breaking stuff).

All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Sat Nov 26 2011 - 21:30:02 PST
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