AMBER Archive (2004)

Subject: Re: AMBER: Improper Torsional Parameters

From: Johnson Agbo (agboj_at_chem.unr.edu)
Date: Thu Jun 17 2004 - 15:57:08 CDT

Dear All;
Thank you all for the timely useful information. Many thanks David and
Carlos.

On Jun 14, 2004, at 2:20 PM, David A. Case wrote:

> 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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