what will be the best way to simulate substrate interaction only within a binding pocket of a large protein.

From: Arun Kumar Subramanian (aksub007_at_gmail.com)
Date: Sat May 07 2011 - 21:20:29 CDT

Hi NAMD'ers,

I am trying to simulate the interactions and conformational changes of a
part of substrate within just one binding site (may be i dont want protein
to be flexible) using NAMD.

But it is still going to take the same amount of computational intensity (if
not, atleast far higher than simulating just few amino acids) if I freeze
the whole protein and allow flexibility only in that region. Moreover I need
to put the protein in a box and fill it with water, that is going to add
more computational cost. Is freezing a good choice if I wish to do this
simulation in a desktop computer with fairly good processor. I just want to
model this in a quick and approximate way. I predict that it might need
around 1-2 days to simulate 1 ns of this protein fully solvated with tip3p
waters in 64 processors in a cluster. Any help or suggestions to accomplish
this will be appreciated.



ArunKumar. S.

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