Dear Neha,
In AMBER the simulation of periodic system is performed with Particle Mesh Ewald algorithm in default, for which all the particles interact with their images.
Have you checked this webpage: http://ambermd.org/tutorials/advanced/tutorial27/pro_metal.htm <http://ambermd.org/tutorials/advanced/tutorial27/pro_metal.htm> ? The example shown and references listed there may be helpful.
Kind regards,
Pengfei
> On Nov 27, 2016, at 11:41 PM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
>
> Dear List,
>
> I have a query regarding simulation of protein at the hydroxyapatite
> surface. I have managed to run the INTERFACE force field in amber (my
> previous post to the mailing list). I want to simulate protein adsorption
> where the hydroxyapatite (HAP) surface is on the bottom side of the box and
> the protein is embedded in water to the lateral sides perpendicular to the
> HAP surface (box size is 113 x 120 x 150 A). I prepare the system with HAP
> and protein interface using various tools in Amber and Gromacs. There is 30
> A layer of water above the protein (I use a cutoff of 12 A) and the HAP
> atoms are constrained using a weight of 2 kcal/mol/A^2. I do a quick NVT
> run and upon visualisation in UCSF Chimera, I could see that the some of
> the atoms of HAP making contact with its own periodic image.
>
>
>
> Is there any way to simulate protein adsorption on a surface/interface in
> AMBER?
>
>
>
> Thank you for kind attention to this material. I look forward to hear from
> you.
>
>
>
> Sincerely,
>
> Neha
>
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Vice Chancellor's Research Fellow,
> Queensland University of Technology,
> 2 George Street, Brisbane, QLD 4000
> Australia
> LinkedIn
> Research Gate
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Received on Mon Nov 28 2016 - 13:30:04 PST
