AMBER Archive (2005)

Subject: Re: AMBER: intramolecular nonbonded interactions in AMBER force field

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Thu Apr 21 2005 - 09:50:24 CDT

> Page 109 and 110 of Amber 8 manual "...Thus the amber mask list is rebuilt
> from these 1-1, 1-2, 1-3,
> and 1-4 pairs......"
> 1-3 and 1-4 are understandable...as nonbonded pairs but 1-1 and 1-2 then
> correspond to self and bonded interaction?? whats the relevance)

    1 4
     \ /
      2---3

1 is self (or 1-1)
1-2 is the bond
1-2-3 is the angle
1-2-3-4 is the dihedral (with rotation around the 2-3 bond).

As Ross Walker pointed out, we "exclude" nonbonded interactions 1-2 and
1-3 interactions since these are included effectively in the bond and
angle parameters. We scale the 1-4 interactions. We completely ignore
self interactions (1-1). This is how it is currently done, although this
does not necessarily mean it is the best or only way. A good example is
with polarization where omitting the short-range bonded non-bonded
interactions (i.e. 1-2, 1-3) may be too severe.

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