AMBER Archive (2004)

Subject: Re: AMBER: distance-aromatic ring

From: Bill Ross (
Date: Thu Feb 19 2004 - 13:41:32 CST

> I would like to study the interaction between the aromatic ring and an
> amine proton. So I would like to follow the changes in distance between
> the proton and the centre of the ring.

Declare a GROUP with the atoms in the ring.
Measure DISTance between proton and group%center.

> I also want to follow the change along the trajectory of the
> angle between the ring normal and the vector joining the
> proton to the ring centre.

It is not so easy to fit a plane to a group of atoms in a general
way, so use PLANE either with 3 atoms in the ring or with 3 GROUPs
of atoms from the ring, e.g. for a 6-membered ring with atoms ABCDEF:
AB CD EF. Then define an AXIS between the proton and the center of
the group containing the whole ring and the plane.

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