Re: [AMBER] Does anyone know how to use nab to generate a single RNA chain

From: Brian Radak <radak004.umn.edu>
Date: Fri, 15 Nov 2013 17:25:30 -0500

I don't know of any program that generates straight chain RNA. What would
be the interest in such a thing?

I suppose you could run some gas phase MD with restraints on the end points
to pull them apart.

Regards,
Brian



On Fri, Nov 15, 2013 at 5:13 PM, v <xiaoli19871216.gmail.com> wrote:

> Yes, However the chain still remain spiral, while what I want is a straight
> chain.
> Thank you
> Li
>
>
> On Fri, Nov 15, 2013 at 2:09 PM, Brian Radak <radak004.umn.edu> wrote:
>
> > Have you tried deleting the complementary sequence?
> >
> >
> >
> > On Fri, Nov 15, 2013 at 5:00 PM, v <xiaoli19871216.gmail.com> wrote:
> >
> > > Hi,all:
> > > I'm trying to use nab to build a single RNA chain for simulation.
> > > However, it seems that all the nab solver are designed to generate
> helix.
> > > Does anyone know how to generate a single RND chain using nab?
> > >
> > > Thanks a lot!
> > >
> > >
> > > --
> > > Li Xiao
> > > University of California, Irvine
> > > Email: xiaoli19871216.gmail.com
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> > >
> >
> >
> >
> > --
> > ================================ Current Address =======================
> > Brian Radak : BioMaPS
> > Institute for Quantitative Biology
> > PhD candidate - York Research Group : Rutgers, The State
> > University of New Jersey
> > University of Minnesota - Twin Cities : Center for
> Integrative
> > Proteomics Room 308
> > Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> > Department of Chemistry : Piscataway, NJ
> > 08854-8066
> > radak004.umn.edu :
> > radakb.biomaps.rutgers.edu
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> appropriate
> > address.
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>
>
> --
> Li Xiao
> University of California, Irvine
> Email: xiaoli19871216.gmail.com
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-- 
================================ Current Address =======================
 Brian Radak                                             :     BioMaPS
Institute for Quantitative Biology
 PhD candidate - York Research Group       :     Rutgers, The State
University of New Jersey
 University of Minnesota - Twin Cities         :     Center for Integrative
Proteomics Room 308
 Graduate Program in Chemical Physics     :     174 Frelinghuysen Road,
 Department of Chemistry                          :     Piscataway, NJ
08854-8066
 radak004.umn.edu                                 :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
_______________________________________________
AMBER mailing list
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Received on Fri Nov 15 2013 - 14:30:05 PST
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