Re: [AMBER] Regarding forcefields for Z-DNA

From: Jiri Sponer <>
Date: Tue, 24 Jan 2017 11:12:35 +0100 (MET)

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

Was it explicit solvent simulation?


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
fax: 420 5412 12179
phone: 420 5415 17133

On Tue, 24 Jan 2017, Yogeeshwar Ajjugal wrote:

> Date: Tue, 24 Jan 2017 15:23:24 +0530
> From: Yogeeshwar Ajjugal <>
> Reply-To: AMBER Mailing List <>
> To: AMBER Mailing List <>
> 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

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