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