AMBER Archive (2006)

Subject: AMBER: Hexahydrated Counterions

From: Mahalakshmi Sahasranaman (mlakshmis_at_gmail.com)
Date: Wed May 10 2006 - 08:22:02 CDT

Dear Amber users,

I have constructed A-DNA (DNA duplex) using nucgen. I want to add
hexahydrated Na+ counterions at a distance of 5 Angstrom to the phosphorous
atom of the phosphate groups.

"addions adna Na+ 0 " only adds Na+ ions. How to add hexahydrated Na+
counterions at a distance of 5 angstrom to the phosphorous atom of the
phosphate groups ?

Thanks,
Lakshmi

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