Re: [AMBER] help with antechamber

From: <>
Date: Fri, 29 Apr 2011 15:52:29 -0400 (EDT)

> I need to make a diatomic CN- (cyanide ion) using a four site model, with
> partial charges on N (-1e at z=1.17Angstrom) C (0e at z=0.0A position) and
> two partial charge sites at 0.22A (-1.31e) and -0.22A (1.31e).

I don't think Amber can deal with a model like this. You have four charge
points that all have to lie on a single line. Both angles and torsions
become degenerate at 180 degrees, so constraining 3 or more points to be
on a line is a tricky proposition with standard force fields.

I think this would require special code to be added to the extra points
section. At least one developer is thinking about a "general" extra
points facility, but that is far from reality.


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Received on Fri Apr 29 2011 - 13:00:04 PDT
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