[AMBER] AMBER Materials modelling- periodic image

From: Neha Gandhi <n.gandhiau.gmail.com>
Date: Mon, 28 Nov 2016 15:41:46 +1000

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

Thank you for kind attention to this material. I look forward to hear from



Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Research Gate
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Received on Sun Nov 27 2016 - 22:00:03 PST
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