On Thu, May 5, 2011 at 12:48 PM, hari krishna <haricoolguy111.gmail.com>wrote:
> 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.
>
See Francois' response.
>
>
> 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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> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu May 05 2011 - 05:30:02 PDT
