[AMBER] metal ion models for Zn+2

From: Fabian gmail <fabian.glaser.gmail.com>
Date: Wed, 4 May 2016 16:10:33 +0300

Dear Amber experts,

I am performing simulations with a protein transporter of divalent Zn+2 ions, that are present in the crystal structure. What I want is to do is to follow or reconstruct if possible the permeation pathway follow by the ions within the transporter. I wonder which ionic model will be the best in this case:

Will be more correct to treat the Zn+2 ions with the bonded or not bonded model?

And additionally which one works with GPUs?

There are four different Zn+2 in the structure, I plan to do one simulation with each of them and see what happens. Is that a good approach?

Thanks a lot,


Fabian Glaser
Head of the Structural Bioinformatics section

Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL

fglaser at technion dot ac dot il
Tel: +972 4 8293701

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Received on Wed May 04 2016 - 06:30:04 PDT
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