AMBER Archive (2001)

Subject: parm warnings

From: Troy Bothwell (tbothwe1_at_bigred.unl.edu)
Date: Wed Mar 28 2001 - 12:48:50 CST

I have recently mutated a 3' terminal base on a 14 mer DNA duplex. Upon
saving the amber parameter files I get the warning

        "Residues lacking connect0/connedt1 - these don't have chain types marked"

>From other errors I received in getting the prep file ready, it seems that
this error comes from the 5' base (DG5) of the complement strand. Because
the mutated base (it actually has a dye attached by phosphate linker on the
terminal OH) no longer has a terminal OH group, I was wondering if the
complement is looking for it? Any suggestions?

Thanks,

Troy