AMBER Archive (2006)

Subject: AMBER: preparing ligand/rna structure for MD

Date: Mon Aug 28 2006 - 13:45:17 CDT

Dear Amber Community,

I am doing some intercalation studies with various nucleic acid structures and
small molecules. I created an intercalation site and used the software Chimera
to dock a molecule of proflavine into the site by hand. What would I need to do
before this structure would be ready for MD? Currently I can not open the file
xleap because I get a fatal bond atom error causing leap to crash.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to