[gmx-users] Query- Advice needed

[Priya Das]

Dear all,

I am working with a membrane bound ion channel. If a ligand binds in the
pore lumen, it occludes the pore and prevent entry of ions.
I have got docking results showing that the ligand binds ion channel.For an
intensive explanation regarding binding of the ligand, i need to prove it
by dynamics studies.
My query is that:

1) Should i simulate the ion channel in DPPC/ POPC membrane so as to get
different conformations of the ion channel (open to closed) and then dock
different models with the ligand?

2) Should i simulate ligand bound ion channel in DPPC/ POPC membrane to
check the stability?

3) Should i use steered dynamics along with conventional molecular dynamics
to show different possible conformations of the ligand along the ion
channel?



-- 
*Let us all join hands to save our " Mother Earth"*
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Regards,
Priya Das
Research Scholar
Dept. of Computational Biology and Bioinformatics,
University of Kerala