Re: [AMBER] improper dihedral torsion parameters for fused rings on tryptophan

From: case <>
Date: Fri, 25 Feb 2011 15:46:42 -0500

On Fri, Feb 25, 2011, Sidney Elmer wrote:
> These happen to be the impropers for the fused rings on tryptophan. Is this
> correct? I have built other molecules where I include these improper angles
> on the fused rings; should I remove them? Thanks for your help.

There was a decision many years ago (probably around 1985) that the
vibrational spectra of purines and tryptophan fit a little better (especially
for the "butterfly" mode) if these impropers were set to zero. But my memory
is that the differences were not great.

This could all be revisted now: in 1985 there were no ab initio quantum
vibrations that were known to be reliable, so most of the compararisons were
made to experimental data, often with uncertainties in the assignments for
out-of-plane bending.

Bottom line: if the difference in behavior between including these impropers
and leaving them out is important to you, there is work to be done. If not,
then worrying about it would be a low priority.


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Received on Fri Feb 25 2011 - 13:00:04 PST
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