AMBER Archive (2005)

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

From: David A. Case (case_at_scripps.edu)
Date: Thu Apr 21 2005 - 10:42:10 CDT

On Thu, Apr 21, 2005, Vineet Pande wrote:

> 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)

This is in the "extra-points" section. For the purpose of counting bonds,
extra points are treated as part of the atom they are connected to. Hence,
you could have a (potential) "1-1" interaction between an extra point and its
attached atom, for example.

This should probably be more clearly explained in the manual. Or, maybe we
should eliminate CHNGMASK as an input variable(?). I don't know of anyone who
has ever used anything but the default value, and I would not be at all
surprised in things broke if you tried setting this to zero.

...regards...dac

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