AMBER Archive (2006)

Subject: Re: AMBER: bad connectivity - more detail

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Wed Dec 27 2006 - 11:44:29 CST

I tried setting the tail, head, connect1, and connect0 with no result :(

Thanks,
SETH

Quoting "David A. Case" <case_at_scripps.edu>:

> On Tue, Dec 26, 2006, Seth Lilavivat wrote:
> >
> > Connectivity - when use antechamber/gaff generated prep residues, I get a
> link
> > from C4 (if it is an A) to O1P or O2 to O1P (if it is a U). The link
> should be
> > from the O2* to the P (since this is a 5' - 2' structure).
> >
>
> Have you tried using the "set" command in LEaP (e.g. set RESIDUE connect1
> O2*,
> where RESIDUE is the name of your modified nucleotide). If so, what was the
> result? (see pp. 64-66 of the Users' Manual).
>
> ...good luck...dac
>
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