AMBER Archive (2006)

Subject: Re: AMBER: 1-4 interaction in AMBER8

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Aug 30 2006 - 16:17:10 CDT

> That means:
> dihedral 1-4 pairs
> 1-2-3-4 1-4
> 2-3-35-36 2-36
> 1-4 pairs are just converted from the dihedral lists.
> Right?
>
> Then what does the EXCLUDED ATOM LIST do?

I think I was wrong about 1-4's - these probably are exactly
as above; it's excluded atoms I was thinking about, which would
be 2 and 3 for atom 1 in the 1st case above. Bond-and-angle
neighbors. The idea being that the bond+angle terms capture the
interactions sufficiently without needing to consider electrostatics.

Bill
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