additional information,
the solution structure contains an internal loop and it is an RNA
molecules.
Thanks again
asaminew
On Mon, Jan 20, 2014 at 12:25 PM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> To what type of molecule ?
>
> For dsDNA, I usually generate B-DNA helices with the bases I want to add
> + 2 additional bases that are identical to the last 2 bases in the
> starting structure on each side
> .
> Then, I superimpose the generated B helices with the starting structure
> using the 2 bases that are identical on each side ... Finally, I merge
> the starting structure with the 2 helices upon keeping only the bases I
> want to add in the 2 helices ....
>
> For dsRNA a similar procedure can be applied but using A-RNA helices ...
>
> For ss nucleic acids its more tricky since you don't have any info on
> the conformation of the bases you want to add ... Probably I would avoid
> adding anything or if really necessary, make a manual guess and start
> simulations with 2-3 alternative models ....
>
> I hope this helps
> Vlad
>
>
> On 01/20/2014 06:09 PM, Asaminew Haile wrote:
> > Dear amber Scientists,
> > I've a solution structure and for stability purpose, I want to append
> more
> > nucleotides to solution coordinate end.
> > Do you have any idea?
> >
> > Thanks in advance
> >
> > asaminew
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
> --
> Dr. Vlad Cojocaru
> Max Planck Institute for Molecular Biomedicine
> Department of Cell and Developmental Biology
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
>
>
> _______________________________________________
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>
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Received on Mon Jan 20 2014 - 10:30:02 PST
