> We dont have anyinitial structure
> and I know that I can use Sirius to manually dock the drug, but,
> where to begin? Outside of the DNA? Starting with the drug already
> intercalated in the DNA? Near the PO4- group?
If the drug intercalates between bases, I would start with it intercalated
because it will probably not achieve that state in normal simulation
times.
Bill
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 24 2009 - 18:09:18 PDT
