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
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Received on Fri Apr 12 2013 - 08:30:05 PDT
