Re: [AMBER] append more nucleotides to solution structure

From: Vlad Cojocaru <>
Date: Mon, 20 Jan 2014 18:25:34 +0100

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

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
> _______________________________________________
> AMBER mailing list

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]
AMBER mailing list
Received on Mon Jan 20 2014 - 09:30:03 PST
Custom Search