[gmx-users] how to obtain binding energy?

[Justin A. Lemkul]

shahab shariati wrote:
> Dear mohsen
> 
> thanks for your reply.
> 
> I forgot to say there are water and ion in my system.
> 
> with new conditions, can I use PMF or TI?
> 

You can use either.

> I have another question:
> 
> is there this possibility to obtain affinity between protein and ligand 
> by gromacs? please guide me about that.
> 

Do you mean binding constants?  If you obtain reliable DeltaG values, then apply 
standard thermodynamic relationships.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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