Dear Himanshu,
Thanks a lot for your reply,
Aas far as I understand, if I use residues from the transporter itself, that will affect the dynamics of the tunnel exit and even can bias the simulation, do you think I can use a water molecule far from the entrance? (so I can allow water to enter the channel and rescue the ion, that is the mechanism I think) and apply to it a large restraint force?
Thanks a lot,
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
> On 5 Jun 2016, at 4:58 PM, Himanshu Joshi <himanshuphy87.gmail.com> wrote:
>
> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Tue Jun 07 2016 - 02:30:03 PDT
