Hi Drs. Walker and Carlos,
Thanks for your suggestions. As correctly pointed out, I have merged two
issues. One is the convergence criteria and secondly I am looking at
protein folding. I am not aware of any papers on use of aMD for disordered
proteins however, my peptide is similar to the system reported by Hamelberg
group (proline rich peptide- *Journal of the American Chemical Society*,
127, 1969-1974 and Biochemistry, 2011, 50 (44), pp 9605–9615).
Prof. Walker: I am applying boost to the whole potential with an extra
boost to the torsions (iamd=3). Do you reconn I should switch to iamd=1?
Many thanks,
Neha
On 12 April 2013 23:10, 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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> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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--
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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Received on Fri Apr 12 2013 - 09:30:03 PDT
