> On Oct 20, 2014, at 12:16 AM, Arun Srikanth <askforarun.gmail.com> wrote:
>
> Thanks i will keep point [1] in mind.
>
> Two questions
>
> In amber,
>
> 1. If I have a dihedral let's say I-J-K-L. How is phi calculated in the
> dihedral potential expression. Is it the angle between the planes
> containing
> I-J-K and J-K-L
Yes. More precisely, it is the angle between the normal vectors of those two planes (which is easy to compute via cross products of the two vectors).
> 2. How is phi defined for an improper I-J-K-L with K as the central atom
Same way.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Oct 19 2014 - 21:30:03 PDT
