Re: [AMBER] Zinc +2 SMD pulling

From: Huang Jing <>
Date: Wed, 4 Jan 2017 12:07:18 +0200

It is diffcult to answer, as it is uncertain what your system/model looks
your system is (Zn2+ + transporter tunnel) and then the SMD is applied to
the whole system ?


On Wed, Jan 4, 2017 at 11:33 AM, Fabian gmail <>

> Hi,
> 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.
> Thanks!!
> Fabian
> 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 - 02:30:02 PST
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