AMBER Archive (2008)

Subject: Re: AMBER: NON-BONDED parameters

From: David A. Case (case_at_scripps.edu)
Date: Mon May 05 2008 - 18:54:32 CDT

On Mon, May 05, 2008, Chih-Ying Lin wrote:
>
> For aromatic systems 1-4 nonbonded interactions are excluded .

I don't believe this is a true statement.

You may be(?) referring to the fact that for a given pair of "para" carbons in a
six-membered ring, there are two ways of making a "1-4" interaction, and Amber
takes care to only include one of the two. But this is not the same as saying
such interactions are excluded.

Generally, force field rules don't know anything about chemical terms like
"aromatic", are they don't (for example) differentiate between nitrogen and
carbon.

...hope this helps...dac

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