Dear David:
I have checked the lib and it contains the 2'methoxy modification but i need
the 2'methoxy 4'aminomethyl modification. How can i generate the forcefied
parameters for this modification.
hari
On Tue, May 3, 2011 at 9:11 PM, David A. Case <case.biomaps.rutgers.edu>wrote:
> 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 Thu May 05 2011 - 04:00:03 PDT
