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
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
http://bku.technion.ac.il
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Received on Wed May 04 2016 - 06:30:04 PDT
