Hi Dear Vlad,
Here is the solution structure
GGCU*aaaa*GGCC
CCGGggggCCGG
final duplex with changed nucleotides with RED color
G*C*CU*aaaa*GG*G*C
C*G*GGggggC*C*CG
I thought I can remove the two end GG/CC and append with GC/CG.
I appreciate your help
Thanks again
asaminew
On Mon, Jan 20, 2014 at 1:53 PM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Sory, but this is very scarce additional information ... It is hard to
> guess how your molecule looks like and what exactly you want to do ...
> I made some guesses already ... If my previous advices don't help, you'd
> have to give more detailed info.
>
> Best,
> Vlad
>
>
> On 01/20/2014 07:14 PM, Asaminew Haile wrote:
> > 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
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> 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
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
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> >>
> > _______________________________________________
> > AMBER mailing list
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> >
> >
>
> --
> 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 - 11:30:03 PST
