[gmx-users] Free energy perturbation enzyme + 5 a.a. Peptide

[Anton Feenstra]

Tivadar Orban wrote:

> Hi,
> 
> I am attempting to calculate the binding free energy, after docking the
> peptide to the enzyme with Autodock.
> Would it be reasonable to use the free energy perturbation method on a
> system composed of an enzyme and a five amino acid peptide? Is the five
> amino acid peptide too large to "grow"?

It may be too flexible. IIRC, there is a very recent paper from the group
of Wilfred van Gunsteren about something like 'Limits to size and flexibility
in the FEP method'. Wait, I may have the reference...

Yes, here it comes:
Single-step perturbations to calculate free energy
differences from unphysical reference states: Limits
on size, flexibility, and character.
C. Oostenbrink and W. F. Van Gunsteren* [ETH]
J. Comp. Chem. 24, 1730-1739 (2003)

OK, so it may be not relevant to FE integration methods (like growing),
but you should have a look anyway, I think.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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