Hello Jason,
Thanks for your answer.
The problem is that when we have a triple bond in amber, then the dihedral
with any of the sp carbons, is the angle between two planes that one of
them can be any arbitrary plane. As the three atoms making this planes are
all on a same line! (That's probably why all their dihedral parameters are
set to zero in amber forcefield), So when I add the fitted dihedral
function (QM-MM0) to my .frcmod, that doesn't reproduce the QM result in
which I have co-planarity due to the electron conjugation. (pretty similar
to diphenyl example in one of your emails). That's why I wanted to define a
dihedral which has a well-defined angle.
About the NMR restraints, I thought as I have built all my forcefieled, by
adding an extra oscillating energy, that might ruin my force field (please
correct me if I'm wrong).
Many thanks again,
Negar
On Mon, Jan 21, 2013 at 6:09 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Your last version of this question was already answered.
>
> Defining a true 'dihedral' for non-serial atoms has non-trivial
> consequences (for instance, the 1-4 scaling factors for the non-bonded
> terms), and the functional form for a the dihedral potential in Amber is a
> number of terms in a Fourier series. What do you really want to do here?
> Do you want to restrain the torsion angle between 4 atoms within a
> particular range? If so, look at the NMR restraint section in the Amber 12
> manual. Even more important, what is the problem you're trying to address?
> What is your hypothesis? And how will your proposed experiment test that
> hypothesis? (None of these questions need to be answered on this website,
> they're just things to think about).
>
> HTH,
> Jason
>
> On Mon, Jan 21, 2013 at 10:32 AM, Negar Ashari Astani <
> negarastani.gmail.com
> > wrote:
>
> > Hello,
> >
> > I had a question on defining dihedral for 4 atoms that are neither in a
> > serial manner nor in an improper manner. There are several other atoms
> > between them. Assuming that I have defined new atom types for these atoms
> > not to confuse amber, does amber apply such dihedral energy?
> >
> > Many thanks in advance,
> > Negar
> >
> > --
> > Negar Ashari Astani
> > PhD student
> > Laboratory of Computational Biochemistry and Chemistry (LCBC)
> > Swiss Federal Institute of Technology (EPFL)
> > BCH 4118 (Bat. BCH)
> > CH-1015 Lausanne
> > Phone: +41 (0)21 693 03 26
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Negar Ashari Astani
PhD student
Laboratory of Computational Biochemistry and Chemistry (LCBC)
Swiss Federal Institute of Technology (EPFL)
BCH 4118 (Bat. BCH)
CH-1015 Lausanne
Phone: +41 (0)21 693 03 26
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Received on Mon Jan 21 2013 - 10:30:02 PST
