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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Dec 31 2006 - 06:07:07 PST
