AMBER Archive (2006)

Subject: Re: AMBER: bad connectivity - more detail

From: David A. Case (
Date: Wed Dec 27 2006 - 10:52:41 CST

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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