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
>>
>>
>> _______________________________________________
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>>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
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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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Received on Mon Jan 20 2014 - 11:00:03 PST
