Dear Daniel,
That sounds very reasonable, and its even better than pushing with a arrow vector in a very sinuous pathway. I looked into the manual and there are many ways of defining restraints and using forces.
Are you aware of any paper that does something similar to what you propose? If you could point me to an example paper or to a good tutorial that does something similar I would more than grateful.
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
> On 4 Jan 2017, at 16:13, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> One thing you could try is pushing the Zn from its initial position
> with distance restraints. These would have to be not too strong,
> otherwise you will end up with a very non-equilibrium pathway. Once
> you have a reasonable looking pathway you could use it e.g. to get
> initial structures for umbrella sampling in order to calculate free
> energy along that path.
>
> -Dan
>
> On Wed, Jan 4, 2017 at 8:09 AM, Fabian gmail <fabian.glaser.gmail.com <mailto:fabian.glaser.gmail.com>> wrote:
>> I am trying to find the permeation pathway of a Zinc+2 ion on a TM transporter, the Zinc is found in the crystal, but the SMD does not work properly, it does not move the ion, or it destroy the membrane protein system if I pull too hard. I have also done 500 ns of normal MD, the Zinc is so charged that I guess the force field electrostatic parameters don’t allow it to move from its initial stable position.
>>
>> QUESTION:
>>
>> Is there an alternative technique to learn about the permeatin pathway of a zinc+2 ion moves through the membrane in AMBER???
>>
>> The initial position of the ion is known…
>>
>> 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
>>
>>
>>
>>> On 4 Jan 2017, at 13:39, Fabian Glaser <fabian.glaser.gmail.com> wrote:
>>>
>>> Sorry I didn't explain it properly, the starting position is inside the tunnel... I want to discover the path the ion takes going out from the tunnel, without pulling.... Nothing happens....
>>>
>>> But i don't know how to do it properly....
>>>
>>> Thanks again!!!
>>>
>>> Fabian
>>>
>>> On Jan 4, 2017 13:34, "Huang Jing" <jing.huang8911.gmail.com <mailto:jing.huang8911.gmail.com> <mailto:jing.huang8911.gmail.com <mailto:jing.huang8911.gmail.com>>> wrote:
>>> In my opinion, it is not necessary to pull the Zn atoms inside the tunnel
>>> artifically; Zn atoms would go inside automatically in the long-time
>>> molecular dynamics procedure, if the transformation is turely happened;
>>> Jing
>>>
>>> On Wed, Jan 4, 2017 at 12:24 PM, Fabian gmail <fabian.glaser.gmail.com <mailto:fabian.glaser.gmail.com> <mailto:fabian.glaser.gmail.com <mailto:fabian.glaser.gmail.com>>>
>>> wrote:
>>>
>>>> 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 <mailto:jing.huang8911.gmail.com> <mailto:jing.huang8911.gmail.com <mailto: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 <mailto:fabian.glaser.gmail.com> <mailto:fabian.glaser.gmail.com <mailto: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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> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb <https://www.lobos.nih.gov/lcb>
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Received on Wed Jan 04 2017 - 07:00:04 PST
