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> 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>> 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>>
>> 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>> 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>>
>> > > 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
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https://www.lobos.nih.gov/lcb
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Received on Wed Jan 04 2017 - 06:30:04 PST
