AMBER Archive (2006)

Subject: AMBER: xleap, generating prep file

From: Seth Lilavivat (
Date: Thu Dec 21 2006 - 10:49:56 CST

Dear Amber Community,

I modified an RNA base in xleap and wanted to save it as a prep file, I have
done this before. After making the changes I did a saveamberprep and received a
message stating "connect1 not defined". When opening the prep file, it only

 0 0 0


What is the proper syntax for setting the connect1 atom? For a nucleoside,
should there be only one UNIT which is contained within one RESIDUE?

Georgia Institute of Technology
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