Re: [AMBER-Developers] AT Manual feedback request

From: case <>
Date: Sat, 26 Nov 2011 12:02:13 -0500

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. 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!


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Received on Sat Nov 26 2011 - 09:30:03 PST
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