AMBER Archive (2005)

Subject: Re: AMBER: How can I read parm99.dat file?

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed May 04 2005 - 19:12:08 CDT

For an unbonded ion, only mass and vdw params need to be defined.
Apparently both are done for I, and the mass line includes a
value for polarizability. The main issue with the parameters
is whether the vdw part is right. Given that there are bond and
angle parameters, the vdw was presumably set for a covalently
bonded I rather than I-, so this value would need to be
overridden with a frcmod entry.

It may not make much difference whether you use Cl- or I- if
the ions are in water.

Some discussion of radii (see 'IONIC RADIUS'):

  http://www.chemguide.co.uk/atoms/properties/atradius.html

And a graph of ionic radii:

  http://www.physchem.co.za/Atomic/Periodicity.htm

Bill
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