Hi,
I also don't think aMD would be applicable for your kind of study.
Considering it was initially disordered, with time you observe the
formation of some secondary structures in normal MD.. but then again, you
are increasing the system's energy, I feel it is definitely going to affect
the folding landscape. If at all the boosting is essential for your study,
after aMD, you should run normal MD simulation for some more time and
observe the folding behavior.
HTH,
Soumya
On Fri, Apr 12, 2013 at 8:40 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Neha,
>
> Further to what Carlos suggests I am not convinced that aMD is a good
> choice of protocol for protein folding simulations which is essentially
> what I believe you are doing here. Firstly if you select your boost poorly
> you can end up just completely unfolding your protein. You might want to
> check the literature and see if anyone has successfully applied aMD to
> disordered proteins and see if there was anything special they needed to
> do. Also are you boosting everything or just the dihedrals? The latter is
> probably appropriate here.
>
> All the best
> Ross
>
>
>
> On 4/12/13 5:59 AM, "Neha Gandhi" <n.gandhiau.gmail.com> wrote:
>
> >Dear Amber users and developers,
> >
> >I have 3 systems with different phosphorylation sites. I am interested in
> >secondary structure analyses of these systems. I am using ff10 force field
> >with tip3p potential. I started conventional MD with disordered structure
> >and after equilibration, ran production for 50ns (NPT) followed by aMD
> >(accelerated MD- dual boost potential as implemented in AMBER12.2 GPU
> >version) runs upto 300ns.
> >
> >I also performed conventional MD for 1 microseconds (same force field and
> >ensemble as above) which showed that system (1) presence of helical
> >structure in the centre; systems (2) and (3) had beta sheets at the N- and
> >C-terminals and no helical structure. These analyses from the trajectories
> >agree with the experimental data.
> >
> >The secondary structure analyses obtained from the aMD runs show that all
> >3
> >systems have similar helical structure for last 50 ns. These doesn't
> >correlate with experimental data.
> >
> >How do I interpret these aMD results? What could be the other parameters
> >which could be looked that? Does aMD has preference for helical structures
> >or is the force field?
> >
> >Your help is appreciated,
> >
> >
> >--
> >Regards,
> >Dr. Neha S. Gandhi,
> >Curtin Research Fellow,
> >School of Biomedical Sciences,
> >Curtin University,
> >Perth GPO U1987
> >Australia
> >LinkedIn
> >Research Gate
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>
>
>
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Received on Fri Apr 12 2013 - 09:30:03 PDT
