I agree, I have never seen anything like this in hundreds
and hundreds of RNA trajectories in explicit solvent,
starting from X-ray structures. Is it explicit solvent?
Implicit could blow up.
Bad starting structure could do it (model building
not based on atomic resolution experiment) even
in explicit solvent.
jiri
-------------------------------------------------------
Jiri Sponer
Professor of Biochemistry
Head of Department of Structure and Dynamics of Nucleic Acids
Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
e-mail: sponer.ncbr.chemi.muni.cz
fax: 420 5412 12179
phone: 420 5415 17133
http://www.ibp.cz/labs/LSDNA/
-----------------------------------------------------------
[ Charset ISO-8859-1 unsupported, converting... ]
> Hi Asfa,
>
> I believe you are already using the best force fields available,so its
> likely that the problem has a different root. Can you give more
> details of your simulation?
>
> Gustavo.
>
> On Wednesday, June 9, 2010, Asfa Ali <asfa.iisc.gmail.com> wrote:
> > Hi,
> >
> > I am using AmberTools 1.3 along with Amber 9 package. I did MD for rna using
> > forcefields leaprc.ff99bsc0 as well as leaprc.ff99SB, however in both the
> > cases the rna structure opens into two strands at the beginning of the
> > production run (without any restraint).
> >
> > What forcefield should I use in order to keep the structure intact?
> >
> > Kindly help.
> >
> > Asfa.
> > _______________________________________________
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> >
>
> --
> Gustavo Seabra
> Professor Adjunto
> Departamento de Qu?mica Fundamental
> Universidade Federal de Pernambuco
> Fone: +55-81-2126-7417
>
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>
>
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Received on Thu Jun 10 2010 - 05:00:03 PDT
