Dear jiri Sponer,
Thank you for your explanation. I have done with explicit simulations and
observed mainly backbone torsion angles
(ε,z,α,γ) changing to B-form.
*Thanks & Regards,*
*Yogeeshwar Ajjugal*
*Ph.D ScholarC/O Dr.Thenmalarchelvi Rathinavelan*
*Dept Of Biotechnology,Indian Institute of Technology Hyderabad,*
*Kandi, Medak-502285.*
On Tue, Jan 24, 2017 at 3:42 PM, Jiri Sponer <sponer.ncbr.muni.cz> wrote:
> It is somewhat unclear, what do you mean by complete transformation
> of Z-form to B-form? I think this has never been achieved by MD except
> of enhanced sampling methods, as it requires syn - anti flips etc.
> To get Z to B transition in MD spontaneosly would be a milestone.
>
> About Z-form, it in general requires (in experiment) specific
> "environmental" conditions. Under normal conditions, B form is
> preferred over Z-form for any sequence, however, due to complexity
> of the transition, the transition is not supposed to be observable in
> MD.
>
> Was it explicit solvent simulation?
>
> 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.muni.cz
> fax: 420 5412 12179
> phone: 420 5415 17133
> http://www.ibp.cz/
> http://www.ibp.cz/en/departments/structure-and-dynamics-of-nucleic-acids/
> -----------------------------------------------------------
>
>
>
>
> On Tue, 24 Jan 2017, Yogeeshwar Ajjugal wrote:
>
> > Date: Tue, 24 Jan 2017 15:23:24 +0530
> > From: Yogeeshwar Ajjugal <bo14resch11004.iith.ac.in>
> > Reply-To: AMBER Mailing List <amber.ambermd.org>
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: [AMBER] Regarding forcefields for Z-DNA
> >
> > Dear amber users,
> >
> > I have performed GPU MD simulations using 2 force fields for Z-DNA
> protein
> > complex , namely 1) ff99SB and 2) combined force field of DNA
> > (leaprc.DNA.OL15) and protein (leaprc.protein.ff14SB) of AMBER16. I
> observe
> > that in ff99SB simulations the Z-DNA conformation remains unchanged
> > whereas, in leaprc.DNA.OL15 specified simulations the conformation of
> Z-DNA
> > is completely transformed to B-DNA conformation. Hence, which of these
> > results is reliable? What should be the appropriate force field to study
> > Z-DNA conformation? It would be really helpful if you could help me out
> > with this issue. Thank you very much.
> >
> > *Thanks & Regards,*
> >
> > *Yogeeshwar Ajjugal*
> >
> > *Ph.D ScholarC/O Dr.Thenmalarchelvi Rathinavelan*
> >
> >
> > *Dept Of Biotechnology,Indian Institute of Technology Hyderabad,*
> > *Kandi, Medak-502285.*
> > _______________________________________________
> > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 24 2017 - 04:30:02 PST
