Re: [AMBER] planarity of Trp side chain and improper torsion term

From: case <>
Date: Sun, 1 Dec 2013 17:23:28 -0500

On Sun, Dec 01, 2013, Jorge Iulek wrote:

> Thanks, Dr. Case, a more technical question might be, from the
> simulation point of view to impose these parameters is needless, yet the
> other imposed torsional angles are enough to take care of that
> planarity, no?

This is correct. "Taking care of planarity" was originally (30 years
ago) judged by agreement with frequencies of out-of-plane vibrational
modes; it might be worth re-visiting that now that high-quality DFT (or
MP2) calculations can be easily carried out on these indole (and purine) ring


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Received on Sun Dec 01 2013 - 14:30:02 PST
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