Hi Hai,
Well I dont know if you can build B RNA with NAB but what you can do is
build a BDNA, modify the PDB and change all the residue names to RNA
specific names (A -> RA, T -> RU, G -> RG,, C -> RC), adapt each T to be
a U (remove the methyl group), load the resulting PDB into Leap which
will add 2'OH groups to all your nts.
Of course, you can do all modifications manually, but probably you'd be
better of if you write a shell script (based on sed, grep and other
useful commands) to do them for you.
Hope this helps
Best
Vlad
On 05/19/2012 06:01 PM, Hai Nguyen wrote:
> Dear Amber experts,
> My apology if the answer for my question is obvious. However, I can not
> find it by myself.
>
> Best
> Hai Nguyen
>
> On Tue, May 15, 2012 at 1:36 AM, Hai Nguyen<nhai.qn.gmail.com> wrote:
>
>> Dear Amber experts,
>>
>> I want to build a series of B form RNA to perform MD simulations showing
>> the conversion from B to A form. However, I can not find a NAB input to
>> build B form RNA (although I can easily build A and B forms for DNA and A
>> form for RNA by a simple NAB input). I've read the Ambertool manual but
>> can't find an easy way to do so (or I may accidentally skip that section).
>> For a single B-RNA structure, I often use this server
>> http://structure.usc.edu/make-na/server.html. However, it's really
>> laborious to build few tens of structures in that way. I really appreciate
>> if you can give me any suggestion. Thanks.
>>
>> Best
>> Hai Nguyen
>>
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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
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Received on Sat May 19 2012 - 10:00:02 PDT
