AMBER Archive (2006)

Subject: Re: AMBER: Impropers definition

From: David A. Case (case_at_scripps.edu)
Date: Wed Mar 29 2006 - 11:10:27 CST

On Wed, Mar 29, 2006, egorov wrote:

>
> J
> |
> K
> / \
> I L
>
> But it's not clear what line improper angle is defined around in above
> figure. As I understand it's only important that central atom of improper
> angle always placed in third position in corresponding lines in parm files
> and order of other three atoms is not a matter. But it may be necessary to
> have exact order of atoms to calculate actual value of improper angle that
> is compatible with Amber parameters.

The rule that LEaP follows is that atoms I, J and L should be in
alphabetical order by their atom *type*. I think ties are broken by sorting
alphabetically on the atom name. You should run some experiments, using
rdparm (or equivalent) to print the dihedrals for some test cases, to make
sure that you understand exactly what you are getting.

....dac

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