Hi Jing,
Thanks for your answer, my system is the Yiip transporter, PDB 3h90, which has crystallographic Zincs, the one I am trying to pull it is indeed inside the tunnel, I really don’t have much experience with SMD, I do have with MD, I am trying to pull only the ion inside the channel to the extracellular side, but I don’t know really what is the correct way to do it, it looks like it is so strongly attached electrostatically to its surroundings, that I need to apply to much force, and the vector in amber is problematic also…
I constructed the system with CHARMM GUI for membrane builders, it worked fine, and a simple simulation of 500 ns also worked fine, but the ion does not move from its initial position. The Zn+2 I am trying to pull is Zn4 on chain A using a dimer. Any suggestion or examples will be more than welcomed.
Best regards,
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
> On 4 Jan 2017, at 12:07, Huang Jing <jing.huang8911.gmail.com> wrote:
>
> It is diffcult to answer, as it is uncertain what your system/model looks
> like;
> your system is (Zn2+ + transporter tunnel) and then the SMD is applied to
> the whole system ?
>
> jing
>
> On Wed, Jan 4, 2017 at 11:33 AM, Fabian gmail <fabian.glaser.gmail.com>
> wrote:
>
>> 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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>>
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Received on Wed Jan 04 2017 - 02:30:05 PST
