AMBER Archive (2006)

Subject: AMBER: what to do with the counter ions when minimizing average structure of DNA?

From: Chengwen Chen (
Date: Tue Nov 14 2006 - 05:09:25 CST

Dear all,

I have get the average structure of a DNA duplex(bound by pt moiety). I plan
to run 500 step of steepest descent minimization in vacuo only for hydrogen
first, and then run 1000 step of steepest descent
minimization using generalized born solvation model for all DNA and counter
ion atoms.

My question is: should I keep the Na+ counter ions from the averaged
structure for minmization? Or I should strip Na+ when average the structure,
and then add counter ions again when running minimization?

BTW, is my minimization steps reasonalble?

Thank you !

Best Wishes


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