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

From: Sidney Elmer <>
Date: Mon, 28 Feb 2011 10:22:10 -0800


Thanks for the historical perspective, it is very helpful. Now that I know
where the warning comes from, I would say that this is not a high priority.
 Thanks for the help.


On Fri, Feb 25, 2011 at 12:46 PM, case <> wrote:

> 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.
> ....dac
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Received on Mon Feb 28 2011 - 10:30:06 PST
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