AMBER Archive (2005)

Subject: Re: AMBER: vdw for terminal phosphate

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri Jun 10 2005 - 13:10:32 CDT

> 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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