RE: AMBER: vdw for terminal phosphate

From: Bill Ross <>
Date: Mon, 13 Jun 2005 13:22:47 -0700 (PDT)

Jonathan, you may be right. I was arguing against an increase beyond
the physically expected size just to solve the interactions of a given
pair. If a physically reasonable radius does not work, I would try
increasing hardness next (which may require readjusting the radius
since well depth (epsilon) is not hrdness per se.

By the way, in one case where an ad-hoc solution was required to
keep atoms from fusing, Peter Kollman recommended using restraints.


> I assert that the terminal phosphate (monoester) oxygen vdw radius would
> be larger than the internal (diester) as there is more charge localized
> on the oxygen atoms (net -2 over 3 oxygen, versus -1 over 2 oxygens).
> The RESP charge for the terminal phosphates is a smidge over -1 (-1.01
> to -1.07) versus -0.77 for the internal phosphate of DNA/RNA. Would
> this additional charge density not mean a larger vdw radius?
> Additionally, the phosphate had too strong of an attraction for multiple
> types of atoms (ARG protons and MG2+), so I would want to have
> parameters that affect its interaction with all atom types.
> Thanks,
> Jonathan Rhoad
> 123 Chemistry
> Life Sciences Post-doctoral Fellow
> Department of Chemistry
> University of Missouri-Columbia
> -----Original Message-----
> > The phosphate oxygens on the sugar phosphates become
> > "attached" to positively charges residues (Mg2+ and ARG) because the
> vdw
> > radius is too small, and electrostatic attraction overwhelms the vdw
> > repulsion term.
> Would increasing the repulsion term 'harden' the oxygens against
> merging? Increasing the radius would affect interactions with other
> atoms. Or perhaps a one-sided distance restraint would do it.
> Bill
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Received on Mon Jun 13 2005 - 21:53:01 PDT
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