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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> 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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Received on Mon Jan 20 2014 - 09:30:03 PST
