Re: AMBER: dihedral angles

From: David A. Case <case.scripps.edu>
Date: Wed, 31 Oct 2007 21:09:24 -0700

On Wed, Oct 31, 2007, Jardas sucuriba wrote:
>
> Hi,I want to use umbrella sampling to rotate a dihedral angle from 110 to
> -55: R | CH3-C1 |
> C2-X I want the direction of the torsion to be such that the CH3-C1 bond
> rotates and not the C2-X. How do I choose this direction?

The torsion restraint only specifies the relative orientation of the first
bond with respect to the second. You can't say which one "moves": that
depends on the forces in the system.

> Another question
> is related with the range of angle values. Should I use positive angles
> (that is from 110 to 305) or from 110 to 0 and then from 0 to -55?

This depends on whether you want to drive the torsion through 180 (trans
orientation of the two outside bonds) or through 0 (cis orientation). There
is no generic right or wrong answer: it depends on your particular system.

If you haven't done such umbrella sampling before, start with an easy, small
system to gain experience, before trying something difficult.

...good luck...dac

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Received on Sun Nov 04 2007 - 06:07:19 PST
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