Another point: it is possible to do a search of the
peptide bond angles to find what is being rotated
in order to agree with a PDB model, but this sort of
defeats the purpose of simple linear rotations.
TBD.
Gordon Chalmers
________________________________
From: Gordon Richard Chalmers <gordoncs.uga.edu>
Sent: Wednesday, December 2, 2020 9:03 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] question about dihedral angles
Thank you for the help in this.
In a protein the phi and psi angles require 2 adjacent
residues. Calculating these angles and rotating is
fairly easy. It is a matter of what is rotated to agree
to a PDB model starting from a linear backbone model.
I will be working the angle rotations further in tleap today,
a little delayed at the moment.
In principle, you should rotate the entire peptide chain
after or before the ith residue as these are bonded in
%% phi C(i-1)-N-CA-C
%% psi N-CA-C-N(i+1)
The actual rotation angle about the intermediary N-CA
or CA-C axis should be the dihedral angle geometrically.
Maybe my own Matlab algorithms aren't correct yet, but
I have checked this many times. I will try to use tleap or
cpptraj instead as a check.
Gordon Chalmers
Department of Computer Science
Complex Carbohydrate Research Center
University of Georgia
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Wednesday, December 2, 2020 8:51 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] question about dihedral angles
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
On Wed, Dec 02, 2020, Karl Kirschner wrote:
>
>impose mymolecule {7} { {C1 C2 C3 C4 120.0} }
One point is this: the command above doesn't specific which atoms are to
be *moved* in order to make the dihderal be 120 degrees. Should the
program move C4 (and atoms bonded to it), or move C1 (and atoms bonded
to it)? Or do something else? This may not be important in some
workflows, but can be key in others.
The pyMol example has the same problem. Of course, its
documentation may be better in explaining what choices are made.
These sorts of manipulations are a natural for NAB (aka "molecular
awk"), but it has its own learning curve and documentation deficiencies.
....dac
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Received on Wed Dec 02 2020 - 06:30:04 PST
