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
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Received on Mon Jan 21 2013 - 09:30:03 PST
