bharat gupta wrote:
Hi,
I want to dock a barrel protein with phosphate ion , to look for the
sites where Phosphate ion binds... I searched the gmx list but I didn't
find much related threads..
You usually won't find instructions specifically tailored for your specialty
application. This list is for general Gromacs usage. Occasionally you'll find
a how-to for something, but that's a rare find.
I want to do the following things...
1) Simulate the binding of phosphate ion with a barrel protein. Here I
do not know where does the ions binds and thats what I want to find
through simulation..
2) After getting the site , I want to look for the binding affinities
between the predicted sites..
I want to know how shall I approach this.. since I don't know how many
ions I have to simulate with the protein..Can anybody help or refer to
some paper??
It sounds like you need to be looking at docking and/or binding site prediction
algorithms, neither of which can be done with Gromacs. Running MD and hoping
your PO4 stick somewhere is a great way to waste time and probably not learn
anything :) There are several ways to calculate binding free energies after
you've determined plausible binding sites.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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