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

From: Giacomo Fiorin (
Date: Tue May 10 2011 - 15:20:18 CDT

Hello Arun, if you freeze most of the protein, you're not gaining much,
because you're still computing all the non-bonded interactions between the
protein and the rest. Also, as you said, you still need to solvate the full
protein with water, most of which would go to waste. Personally, I'd much
rather leave the whole protein free to move, if you have it.

Or, if you really need something "quick and dirty", I would suggest cutting
away most of the protein altogether and keep only the binding pocket, which
you can then solvate with a much smaller water box. Since this is just a
fragment which could lose quickly its fold, to keep it in place you may use
harmonic position restraints (keyword: constraints) rather than freezing
(keyword: fixedAtoms).


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  Giacomo Fiorin - Postdoctoral Researcher
  ICMS - Institute for Computational Molecular Science - Temple University
  1900 N 12 th Street, Philadelphia, PA 19122
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On Sat, May 7, 2011 at 10:20 PM, Arun Kumar Subramanian

> 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.
> Thanks.
> Sincerely,
> ArunKumar. S.

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