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
--
========================================
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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