Dear all,
The formation of B-Z junction is provoked by many conditions including the
presence of A...A mismatches, as reported by Khan et al in Plos
Computational Biology ( DOI :10.1371/journal.pcbi.1004162). I observe that
in ff99SB forcefield my DNA which has B-Z junction initially remains
unchanged till the end of the simulation, whereas in leaprc.DNA.OL15
forcefield the structure is moving more towards B-conformation at the end
of the run. Thus, I want to know which would be the appropriate forcefield
to study the formation of Z-DNA. Thank you.
*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 5:31 PM, Yogeeshwar Ajjugal <
bo14resch11004.iith.ac.in> wrote:
> 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 Thu Jan 26 2017 - 06:00:02 PST
