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

From: Bill Ross <>
Date: Wed, 4 May 2005 17:12:08 -0700 (PDT)

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'):

And a graph of ionic radii:

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Received on Thu May 05 2005 - 01:53:00 PDT
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