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
>
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Received on Tue Jan 24 2017 - 02:30:03 PST
