Re: [AMBER-Developers] AT Manual feedback request

From: B. Lachele Foley <>
Date: Sun, 27 Nov 2011 04:43:54 +0000

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.

We recently ran into trouble with this as we've begun to build more complex structures in a greater variety of conformations. We had previously believed that "impose m {5 4} ..." only made its imposition on atoms within residues 5 and 4. Alas, 'twas not the case.

The impose command doesn't do anything to an improper torsion, best I can tell. Every time I tried, it silently did nothing when instructed to "impose" on any four atoms that are not sequentially bonded.

:-) Lachele

Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA

From: Yong Duan []
Sent: Saturday, November 26, 2011 10:44 PM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] AT Manual feedback request

Would it work better if the selections are more explicit, using the syntax
of ptraj/cpptraj?
Although the typical convention uses CA to identify the residues of the
quartet in cases of PHI and PSI, in some cases, it's not easy to devise a
reasonable convention.

For example, in the {N C CA CB} quartet case, which one we actually meant
to? Is it .N:3 .C:3 .CA:3 .CB:3 (which is an improper), or, .N:4 .C:3
.CA:3 .CB:3, which is PSI' (differing from PSI by about 120 degrees).
Right now, I think leap interprets as later.

A side note: "impose" sounds more like an energy penalty function that may
take effect in simulations. More intuitive commands might be something
like rotateto or just plain "torsion" since it only affects the structure,
not prmtop.

On 11/26/11 9:02 AM, "case" <> wrote:
>On Wed, Nov 23, 2011, B. Lachele Foley wrote:
>> I have come to believe that the behavior of the impose command is
>> deliberate though it would never have occurred to me to write it that
>> way.  Because my viewpoint is sufficiently different, I also would never
>> have understood the proper behavior from reading the manual.  So I added
>> some info based on how I have observed it to behave.
>Thanks! Maybe even more verbosity in the explanations would help.  For
>impose peptide { 3 } { { N C CA N -40.0 } }  # affects residues 3 and 2
>I think you mean "affects the *internal* coordinates of residues 3 and 2;
>I'm thinking this really means that it changes psi in residue 2 to -40.
>that correct?  If so, saying that explicitly might help.  And, what
>happens to
>the CB group of residue 2 when you do this?  OR, suppose you have the
>following command:
>impose peptide { 3 } { { N C CA CB -40.0 } }
>Does this change the backbone psi angle as well?
>[To beat to death my earlier complaint: all these questions seem to arise
>because the "impose" command is trying to be too terse.  Alternatively, we
>need to be able to explain in some detail what chemical assumptions LEaP
>making when it carries out an impose command.]
>Is impose working strictly in internal coordinates?  What happens to the
>cartesian coordinates, e.g. that savePdb would produce?  In cartesian
>coordinates, the above impose command might alter the coordinates of
>1, or residue 4, or both (but not neither).  Understanding what happens
>be helpful; or maybe the answer is that the overall orientation of the
>following an impose command is very difficult to predict or explain, and
>people should not rely on any particular behavior in that respect.
>Finally, some examples of what the sequence command does at link points
>also be helpful.  Just trying take advantage of your experience here!
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