On Tue, May 03, 2011, hari krishna wrote:
>
> I need to do the simulation of the modified oligonucleotides in mRNA. The
> modification is 2'-methoxy 4'-aminomethyl uridine, what is the force field I
> can use for the simulation. Is there is any force field for this specific
> modification. And also what are the things necessary to take care while
> doing the modified RNA simulation
Have you checked the modified RNA library in
$AMBERHOME/dat/leap/lib/allmodrna08.lib (and a corresponding frcmod file)?
This has many modified bases, and may either have what you want or something
close. Please see section 2.7 of the AmberTools Users' Manual for further
info and references to the original papers.
....dac
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Received on Tue May 03 2011 - 09:00:02 PDT
