AMBER Archive (2005)

Subject: RE: AMBER: vdw for terminal phosphate

From: Rhoad, Jonathan S. (rhoadj_at_missouri.edu)
Date: Mon Jun 13 2005 - 11:21:49 CDT

Bill,

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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