Re: [AMBER-Developers] AT Manual feedback request

From: Yong Duan <duan.ucdavis.edu>
Date: Sat, 26 Nov 2011 19:44:29 -0800

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. 


--
yong
On 11/26/11 9:02 AM, "case" <case.biomaps.rutgers.edu> 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
>example:
>
>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.
>Is
>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
>is
>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
>residue
>1, or residue 4, or both (but not neither).  Understanding what happens
>might
>be helpful; or maybe the answer is that the overall orientation of the
>system
>following an impose command is very difficult to predict or explain, and
>that
>people should not rely on any particular behavior in that respect.
>
>Finally, some examples of what the sequence command does at link points
>would
>also be helpful.  Just trying take advantage of your experience here!
>
>...thx...dave
>
>
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Received on Sat Nov 26 2011 - 20:00:02 PST
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