Re: [AMBER] flag dihedrals in the .prmtop

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 29 Dec 2010 01:24:04 -0700

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
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