[gmx-users] bindng energy & H bond energy calculation

[Justin A. Lemkul]

On 7/3/12 2:24 AM, Ravi Raja Merugu wrote:
> Dear all,
> Can any one help e regarding
> 1.)  I want to find the binding energy of  ligand with the protein , and

Umbrella sampling or free energy calculations can determine binding energies.

> 2.)  Hydrogen Bond energy of the protein ligand interactions  (for
> H-bond ).. and

This term will probably be related to electrostatic interactions, but I don't 
know of any way to directly extract a "hydrogen bonding energy" in a literal 
sense.  Most force fields don't include such a term.

> 3 )  if possible H bond distances along the time scale(say 10ns).
> Is there any way

g_dist and/or g_hbond

> 4 ) to measure the contribution of hydrophobic / philic interactions
> of the protein active site with ligands binding energy..

Free energy calculations, decoupling van der Waals and Coulombic terms 
separately, will tell you this information.

> 5) to calculate the distance between the residues(let say Tyr and Arg)
> in my protein. (Actually I want to check a  key interaction between
> them)

g_dist

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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