AMBER Archive (2004)

Subject: AMBER: Solvent exposure measurement

From: Yuqin Cai (
Date: Fri Nov 05 2004 - 13:32:22 CST

Dear Ambers,

I am trying to look into the differential hydration of BP ring system which attached to two different sites of G of a 12mer DNA duplex. I've done the simulation using Na + conterions and explicit waters.  I wonder if there is a way to get the solvent exposure of the aromatic moiety directly form Amber. And is there any way to get the solvent exposure as a function of time ?

Thanks a million


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