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 - 04:30:02 PDT
