Thanks, I have worked out the correct notation now, but I think maybe they
are terminal atoms. The O3T atoms only occur on the final residues of the
DNA. I will try changing those atoms to the O3' ones that occur in the
middle of the DNA. I'm not sure if that will work.
>From: Bill Ross <ross.cgl.ucsf.edu>
>Reply-To: amber.scripps.edu
>To: amber.scripps.edu
>Subject: Re: AMBER: Ring of dna
>Date: Fri, 14 Jul 2006 10:23:07 -0700 (PDT)
>
> > bond ade.1.P ade.94.O3T
>
>You have to start names with the unit name for the whole system,
>and use literal residue names like in the pdb. Also I believe
>O3T implies you are trying to bond off a terminal residue which
>is wrong.
>
>Bill
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Received on Sun Jul 16 2006 - 06:07:10 PDT
