[gmx-users] Why h_bond can not form

范聪 fanc232 at nenu.edu.cn
Mon May 11 02:48:59 CEST 2015

Hello everyone!

I offered a picture called "ask.png" to illistrate my question.

 According to the referense papers, the H atom of the -OH group of TYR306 should form H_bond with the carbonyl O atom of the ligand.
 But in my simulations, the H atom turned after a very short time, towards the side chain of PHE152.
I guess the reason is that, first, the positive Zn ion near the ligand's carbonyl O atom made a repulsive effect against the H atom in -OH group; second, the π-electron cloud of the side chain of PHE attracted the H atom in the -OH group of TYR306.
 As a whole, I failed to make out a real-enough simulation because the h_bond between the ligand and TYR306 did not form.

 Also I have one more question: Is there any tools or solutions to calculate the hydrophobic or π-π interactions between the ligand and seleted residues of the protein, so I could make a graph of the interactions against time?

Any suggestions willl be of great help, Thanks!

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