Re: [AMBER] Chirality of amines in GAFF

From: David A. Case <>
Date: Wed, 14 Apr 2010 18:34:01 -0400

On Wed, Apr 14, 2010, Dean Cuebas wrote:
> Is it normal for the MD code to allow protonated tertiary amines to
> invert??? The bottom line is that it shouldn't.

The situation is comparable to inversion about tetrahedral carbon atoms: under
"ordinary" conditions, there is no problem. But people run simulated
annealing runs at hundreds (or thousands) of degrees, and may include
artificial forces, or start from very strained geometries. In such cases, the
usual ideas from what happens in the real world become irrelevant.


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Received on Wed Apr 14 2010 - 16:00:04 PDT
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