Re: [AMBER-Developers] AT Manual feedback request

From: B. Lachele Foley <lfoley.uga.edu>
Date: Sun, 27 Nov 2011 20:43:59 +0000

>What I meant by "improper" was that the order of the atoms can imply an
> improper torsion. I think (.N:3-.C:3-.CA:3-.CB:3) is actually an improper
> torsion (CA connects to all three other atoms). But, I think Dave meant
> .N:4-.C:3-.CA:3-.CB:3 instead, which is a proper torsion, is actually the
> PSI' torsion. The difference is just .N:4 vs @N:3.

I didn't do comprehensive testing yet, but from what I observed so far, let's say you specify

impose m {4} {A B C D 30.0}

Leap goes to residue 4 and finds an atom called "A". It then looks for an atom called "B" that is bonded to A without regard to the identity of the residue that contains B. If it doesn't find a bonded atom, B, it stops. If it finds one, it looks for C bonded to B and D bonded to C in the same manner. Then, it applies the torsion around the B-C bond. So, it wouldn't act on an improper torsion because at some point it won't find a bond.

:-) Lachele

Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA
lfoley.uga.edu
http://glycam.ccrc.uga.edu

________________________________________
From: Yong Duan [duan.ucdavis.edu]
Sent: Sunday, November 27, 2011 2:57 AM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] AT Manual feedback request

Agree with both. Extension is a much better approach than changing. So,
let "impose" do whatever it has been doing. We just add a couple of other
more intuitive commands, with more specific masks, etc. As for mask, the
leap mask would work, so long as it allows the users to explicitly choose
the atoms they want to manipulate. Adding ptraj/cpptraj masks would be
great, though :).

What I meant by "improper" was that the order of the atoms can imply an
improper torsion. I think (.N:3-.C:3-.CA:3-.CB:3) is actually an improper
torsion (CA connects to all three other atoms). But, I think Dave meant
.N:4-.C:3-.CA:3-.CB:3 instead, which is a proper torsion, is actually the
PSI' torsion. The difference is just .N:4 vs @N:3.

Speaking of extension, I am thinking perhaps sometime down the road we may
want to consider extending the commands to "cmd target option" syntax. For
example save{pdb, amber, off, parm, pol} etc., would be grouped together.
This is not an important issue, just a bit convenience (but I guess that's
user interface made for :) ).

--
Yong Duan, Ph.D, Professor
UC Davis Genome Center and
Department of Biomedical Engineering
University of California at Davis
Davis, CA 95616
530-754-7632
On 11/26/11 9:06 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
>
>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
>
>--
>Jason M. Swails
>Quantum Theory Project,
>University of Florida
>Ph.D. Candidate
>352-392-4032
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Received on Sun Nov 27 2011 - 13:00:03 PST
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