AMBER Archive (2006)

Subject: AMBER: Impropers definition

From: egorov (egorov_at_newhospital.ru)
Date: Wed Mar 29 2006 - 00:06:40 CST

Dear All,

I want use Amber force fields in my own energy function for internal use.
But I was not able to find exact Amber definition for improper angles. In
Scientific Background of Amber Manual showed spatial definition of improper
quartet of atoms :

                                   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. So how can I obtain such a sequence of
four atoms to do this calculation?

Thank you very much for your attention to my problem.

D. Yegorov,
Department of Clinical Laboratory and Microbiological Diagnostics
Ural State Medical Academy.
620219 Russia, Repin str., build. 3

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