[gmx-users] Binding energy for two proteins

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 15 01:27:48 CET 2010

jorge_quintero at ciencias.uis.edu.co wrote:
> Dear all.
> A few days ago I posted a question related with binding energy between two
> proteins using the LIE method, in that case my energies were between -2400
> to -2700 kcal/mol.  Later, I tried to obtain the same information doing
> several simulations employing the FEP method in combination with ffamber94
> force field, only I used one of the complex model obtained with a docking
> tool (protein-protein).  with the FEP method my energy is completely
> different compared to the LIE method.
> result with LIE:  -2600 kcal/mol
> result with FEP:   7400 kcal/mol
> What happen with these result.  I guess these results might be slightly
> the same.  isn't it?.  I'll appreciate your support.

I don't know how reliable decoupling an entire protein will be (nor do you give 
any details about your protocol, precluding any assessment of its reliability), 
but there may be significant error bars.  Another technique that you might 
consider is the calculation of PMF using the pull code.



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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