AMBER Archive (2000)

Subject: Leap problems with Zn, DNA

From: Michael Cooney (mike_at_bmbiris.bmb.uga.edu)
Date: Tue Sep 05 2000 - 16:59:54 CDT

Hello everyone,

I have still been having problems with Leap in Amber 6.
It will add protons to the peptide part of a protein:DNA complex
but does not recognize the third oxygen on terminal 5' phosphates on the
DNA, and also the default atom database does not seem to include zinc.
Any suggestions for these atom types would be appreciated.

Thank you!

Sincerely,

Michael Cooney
Department of Biochemistry and Molecular Biology
The University of Georgia
Athens, GA 30602