[AMBER] Zinc +2 SMD pulling

From: Fabian gmail <fabian.glaser.gmail.com>
Date: Wed, 4 Jan 2017 11:33:29 +0200


I am trying to perform SMD with a Zinc +2 ion inside a transporter tunnel, but either the Zn does not move at all, or if apply too much force the system is destroyed, or I am doing something wrong….

Can anyone please direct me to some good paper using amber for this specific purpose?
Meaning trying to pull an ion from its initial X-ray position out of the transmembrane region of a transporter?

I am starting to think that amber is not well suited for treating this specific question or that the forcefield parameters for Zn+2 are not good enough. Another thing that is probably making the work more difficult is that the vector I am using to pull is centered in a water molecule on the approximate direction of the channel exit, but obviously the channel is not a vector…

Anyway any paper or review or information that could help me to make this experiment more correct will greatly help me.



Fabian Glaser PhD
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, Israel

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Received on Wed Jan 04 2017 - 02:00:03 PST
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