Thanks Vlad,
Hai
On Sat, May 19, 2012 at 12:48 PM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> 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
> >>
> > _______________________________________________
> > 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
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun May 20 2012 - 08:30:03 PDT
