Hi Fabian,
I think its not necessary to define dummy atom. You can specify
an atom or a group of atoms in the direction where you want to
pull the ions. Next, use the distance restraints between the ions and
group in that direction. Apply high harmonic restraints to that group so
that ions can move in the desired direction. I hope that will solve you
purpose.
AMBER manual and mailing list also have useful discussion regarding SMD
protocols,
Here is one tutorial on SMD simulation in AMBER,
http://ambermd.org/tutorials/advanced/tutorial26/section2.html
HTH
With Regards
Himanshu Joshi
On Sun, Jun 5, 2016 at 4:59 PM Fabian gmail <fabian.glaser.gmail.com> wrote:
> Hi,
>
> I am trying to figure out what is the best strategy to pull a zn+2 ion
> from a membrane embedded transporter, the Zn+2 ion is present in three
> different locations on the transporter, and I want to pull it through the
> transporter towards the periplasm. One location in each simulation. Initial
> regular MD of 500 ns didn’t show any migration of the ion, probably the
> force field parameters are making for it difficult to move from its highly
> negatively charged environment (?)
>
> So I am thinking to apply force on the ion to help it moving out of its
> initial location with SMD. I looked into the tutorial on SMD, but as far as
> I saw, there are not tutorials showing pulling strategies for ions.
>
> Should I use a dummy atom outside the membrane?
>
> I prefer not to use this strategy, since I will need to use a water
> molecule and keep it on its place with a very strong force constant. Is
> there a better way?
>
> Can the atom be pulled towards the transporter exit with a vector? What is
> the correct way of doing this?
>
> Can you please recommend me a tutorial or a correct strategy with Amber15
> on this matter?
>
> Thanks a lot in advance,
>
> Fabian
>
>
> Fabian Glaser
> 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 32000, ISRAEL
>
> fglaser at technion dot ac dot il
> Tel: +972 4 8293701
> http://bku.technion.ac.il
>
>
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Received on Sun Jun 05 2016 - 07:00:03 PDT
