[gmx-users] how to calculate binding free energy and electrostatics potential for ligand-protein complex

[Justin A. Lemkul]

pawan gupta wrote:
> hello
> 
> How can we calculate binding free energy and electrostatics 
> potential  for ligand-protein complex?

Binding free energy may require the calculation of PMF or the use of 
thermodynamic cycles (both somewhat complicated procedures).  If you want the 
nonbonded energies between the protein and ligand, simply use energygrps, but 
these values will not correspond to binding free energy.  You may also be able 
to use g_lie, but you will still have to set the appropriate energygrps and have 
some idea about the parameters to set of -Elj and -Eqq.

-Justin

> 
> which parameter is required in mdrun input file for that?
> 
> I tried online manual but did not get output.
> 
> It is appriciable if any body have idea
> 
> 
> Thanks in advance
> 
> 
> Regards
> Pawan Gupta
> 

-- 
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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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