I know you people, Carlos, from SB NY. You are supposed to work first
and then talk. Figure it out before saying it is possible or not.
Gordon Chalmers
________________________________
From: Gordon Richard Chalmers <gordoncs.uga.edu>
Sent: Wednesday, December 2, 2020 6:08 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] question about dihedral angles
By the way, are you sure the angular rotation is about the
2 middle atoms in the 4 bond. That would be good to know if
writing your own code.
Gordon Chalmers
________________________________
From: Gordon Richard Chalmers <gordoncs.uga.edu>
Sent: Wednesday, December 2, 2020 5:58 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] question about dihedral angles
Why don't you try this then: given phi psi angle information of
pdb and a linear peptide of its form, reconstruct the pdb file.
The problem is not due to numerical instability of the phi/psi
angle computation; phi/psi angles are important physically.
Gordon Chalmers
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Wednesday, December 2, 2020 5:52 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] question about dihedral angles
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
I think that even if you have a list of phi/psi pairs and their values,
it's pretty well known that small angle variations can result in large
Cartesian changes far from the bond being rotated. I'm not saying this
isn't a good plan, but you may run into issues (as you say) with non-planar
groups giving small changes in the intended dihedral and leading to
significant changes farther down the chain.
You should be able to put together a cpptraj script by listing the atom
names/residues in dihedral commands to measure them from your pdb, then
building a cpptraj script to rotate.
Dan's documentation is quite good for academic code standards and I don't
think you'll need him to make the inputs for you.
tleap can do similar things with commands such as "impose", and in the end
it should matter which part gets rotated if you have a single molecule,
since all that will be affected is the overall rotational frame of
reference. If that is important though, then Dan's suggestion is worth
trying. There may be other codes that were intended to build structure
models, Amber doesn't really have extensive tools for that purpose.
On Wed, Dec 2, 2020 at 5:41 PM Gordon Richard Chalmers <gordoncs.uga.edu>
wrote:
>
> Hi Daniel,
>
> How about giving me a known PDB protein model and a sequence of
> rotations to bring its linear form into it? That would be a benefit,
> Either
> in tleap or cpptraj.
>
> I think I know what the issue is with non-parallel planes from
> the 2 pairs of 3 atoms in the 4 bond of the peptides.
>
> Gordon Chalmers
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Wednesday, December 2, 2020 11:50 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] question about dihedral angles
>
> [EXTERNAL SENDER - PROCEED CAUTIOUSLY]
>
>
> 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 02 2020 - 16:30:02 PST
