AMBER Archive (2004)

Subject: AMBER: PARSE radius for P

From: david.evans_at_ulsop.ac.uk
Date: Thu Jun 10 2004 - 12:59:30 CDT

Hi,

In the Sitkoff et al. article on PARSE (J.Phys.Chem. 1994, 98,
1978-1988)
there is no radius parameter for phosphorous. The ptraj utility is
coded to produce 2.0.
I was wondering where this value came from.

I'm doing a binding energy calculation using DelPhi and MM-PBSA, and
I expect it is not overly important for phosphate groups in DNA,
since the oxygens are closest to the surface, but if anyone has
experimented with changing the P radius it would be interesting to
hear about it.

Thanks,

Dave Evans


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