AMBER Archive (2004)

Subject: Re: AMBER: Improper Torsional Parameters

From: David A. Case (case_at_scripps.edu)
Date: Mon Jun 14 2004 - 16:20:21 CDT

On Mon, Jun 14, 2004, Johnson Agbo wrote:

> The manual for amber 7 together with ref. 13 gave the formula used in
> the calculation of the torsion or dihedral angles but no relation is
> given for the improper torsion. How then are the improper torsions
> calculated or they are not necessary for work in Amber.

The functional form for "improper" torsions is the same as for "proper"
torsions, hence the distinction is for many purposes academic. A proper
torsion is one that for which covalent bonds exist between atoms 1-2, 2-3,
and 3-4; otherwise, the torsion is called an improper one.

LEaP requires that parameters be available for all proper torsions. In
addition, it tries to assign improper torsions to all atoms with 3
substitutents. It will make the assignment if there is an appropriate
paramter, otherwise it will (silently) skip that set of atoms. You can use
the "verbose" flag to warn you about missing improper parameters for sp2
atoms.

...hope this helps...dac

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