On Wed, Dec 29, 2010 at 12:43 AM, Z.Xiao <zfengxiao.126.com> wrote:
> Hi all,I'm a fresher for amber. I am puzzling over the flag dihedrals in
> the .prmtop file.
> for example,the dihedral 3 6 9 12 had two definitions,3 6 9 12 4 and 3 6 -9
> 12 5 in my .prmtop
> file.Here 4 and 5 represents different dihedral types obviously.Which is
> appropriate? or was
> the dihedral descriped by the sum of the two cosine functions above?
>
This indicates that it is a multi-term dihedral (or part of a ring system).
See
http://ambermd.org/formats.html for a description of the prmtop file
which was recently updated.
Good luck!
Jason
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Dec 29 2010 - 00:30:03 PST
