AMBER Archive (2008)

Subject: Re: AMBER: Dihedral Angle Parameters

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Jun 26 2008 - 17:07:55 CDT

Dear Carlos,

Yes, I mean symmetry about 0. For instance the alfa-dihedral angle for the
RNA is defined with the following parameters:

OS-P -OS-CT 1 0.25 0.0 -3. JCC,7,(1986),230
OS-P -OS-CT 1 1.20 0.0 2. gg&gt ene.631g*/mp2

The E_torsion energy function for this dihedral is symmetric about 0. If I
add another paramater list for this dihedral angle (with a non-zero
phase), it can become asymetric. However, I am not sure if this is allowed
in amber force field. Thanks.

Best,

On Thu, 26 Jun 2008, Carlos Simmerling wrote:

> symmetric about what? if still a cosine term, then it has an intrinsic symmetry.
> by varying phases, you can change symmetry about 0 if that's what you mean.
>
> On Thu, Jun 26, 2008 at 5:07 PM, Ilyas Yildirim
> <yildirim_at_pas.rochester.edu> wrote:
> > Dear AMBER users,
> >
> > I realized that the amber dihedral parameters are symmetric; the torsional
> > energy vs angle has a symmetric character. Is it reasonable to create
> > dihedral parameters for a particular dihedral angle such that it will have
> > an asymmetric torsional energy function in amber force field? Thanks in
> > advance.
> >
> > Best,
> >
> > --
> > Ilyas Yildirim
> > ---------------------------------------------------------------
> > = Department of Physics - =
> > = University of Rochester - =
> > = 585-275-6766 (office) - 585-267-5644 (home) =
> > = http://www.pas.rochester.edu/~yildirim/ =
> > ---------------------------------------------------------------
> >
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  = Department of Physics        -                              =
  = University of Rochester      -                              =
  = 585-275-6766 (office)        - 585-267-5644 (home)          =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------

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