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Justin A. Lemkul jalemkul at vt.edu
Sat Feb 12 14:20:51 CET 2011

mohsen ramezanpour wrote:
> Dear All
> I want to evaluate the binding free energy of protein-dryg.
> My protein has so many atoms(5000 atoms),it make running too long.
> I want to use Umbrella sampling for this.
> Can I separate active site of protein (a radious of 3 nm around of my 
> drug )and do my work on this system?

I would think that such a fractured system would suffer from a number of 
unpredictable artifacts.  Protein structure is fairly sensitive, so you'd have 
to apply lots of artificial restraints to preserve geometry, but then what if 
even small conformational changes are needed to for the protein to properly bind 
the drug?

Umbrella sampling is one of the more laborious ways of calculating binding 
energies.  Free energy cycles would probably be significantly more efficient, 
since you can use a smaller box size and (in all likelihood) run shorter 
simulations that still converge.


> Thanks in advance for your guidances.
> Mohsen


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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