Dear experts in Amber users group
I performed a 20 ns MD simulations of a ligand-protein complex system.
The ligand binding free energy was calculated using MMGBSA.
The energy was decomposed onto residues in the binding pocket for identifying residues important for ligand-protein interactions.
Now I have difficulties to interpret the decomposition result, as it suggested Threonine 119 is critical for both polar & non-polar interactions.
Here is the part of the result:
Resides van der Waals Electrostatic Polar Solvation Non-Polar Solvation TOTAL
Thr119 -1.21 -2.37 0.27 -0.93 -4.23
But Threonine is a polar residue and it is seldomly contributes to hydrophobic interactions, as I was taught during biochemistry course.
Could you please help me figure out where the problem is?
Thanks a lot for your help!
Cheers
Marc
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 08 2016 - 09:30:03 PST
