[gmx-users] bindng energy & H bond energy calculation
Justin A. Lemkul
jalemkul at vt.edu
Tue Jul 3 11:39:08 CEST 2012
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
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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