AMBER community:
I am modeling sugar phosphates in AMBER and NAMD with parm99. The
charges for the sugar phosphates were derived according to Cieplak, et
al. The oxygens on internal phosphates (phosphate diesters) in DNA and
RNA have van der waals parameters that are the same as C=O, and have
similar charges. Because the sugar phosphates have phosphate
monoesters, the charge on the oxygen is much larger that the phosphate
diester. 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. What is the best way to calculate/estimate proper vdw
radii for new residues? How were the original vdw radii detemined? I
have crystal structures that I can use to estimate the proper
equilibrium distance, but am unsure how to take the electrostatic
attraction into account when defining the vdw radius. Should I just do
trial and error until I can reproduce the average crystal structure
distance in a minimization?
Thanks,
Jonathan Rhoad
123 Chemistry
Life Sciences Post-doctoral Fellow
Department of Chemistry
University of Missouri-Columbia
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Jun 10 2005 - 17:53:00 PDT
