Hi,
The command for calculating dihedral angles in cpptraj is 'dihedral'.
The command for rotating atoms around a dihedral is 'rotatedihedral'.
Both are documented in the manual. The convention in cpptraj is for
all atoms connected to the greater atom index to move; those connected
to the lower atom index are fixed. Cpptraj does the rotation in
Cartesian space - I think tleap may do it via internal coordinates but
I'm not sure about that.
-Dan
On Wed, Dec 2, 2020 at 9:04 AM Gordon Richard Chalmers <gordoncs.uga.edu> wrote:
>
>
> 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 - 09:00:02 PST
