AMBER Archive (2006)

Subject: AMBER: Parameterization of ethidium - phenyl ring

Date: Thu Sep 28 2006 - 15:02:08 CDT

Dear Amber Community,

I am doing some MD using ethidium in one of my models and I have had some
trouble getting the phenyl ring to "behave" correctly. The phenyl ring sits
coplaner to the rest of the molecule where it should be 45 - 60 degrees I
believe. Is there an appropriate atom type I can assign as a solution? If not
what would I have to do?

Georgia Insitute of Technology

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