Re: parm warnings

From: Bill Ross <>
Date: Wed 28 Mar 2001 11:58:17 -0800 (PST)

        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 chaintypes marked"

The only consequence of not having chain types marked
is that you can't use the TORSION BACKBONE function in

If you want this, you need to set the connect atoms in
the residue definition. E.g. for a new residue MUT:

> loadamberprep MUT.prep
> set MUT.1 connect0 MUT.1.P
> set MUT.1 connect1 MUT.1.C3'
> saveoff MUT MUT.lib

        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

No - it is from a nonstandard residue.

        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?

Leap knows nothing of complementarity of strands.

Bill Ross
Received on Wed Mar 28 2001 - 11:58:17 PST
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