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PostPosted: Thu May 29, 2014 3:34 am 
Millimolar User
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Joined: Thu May 29, 2014 2:59 am
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I have done docking using Autodock. In the results I found that the best conformation for ligand and receptor doesnot have any H bonds between them.
1. Is it possible to have such conformations?
2. What could be the reason?
3. What conformation should I consider, the one with more H bonds between ligand and receptor ? or the one with highest binding enery(which dont have any H bonds)?

In the literature, I found that the same ligand and protein have 3 H bonds were observed with Moldock. The protein structure from PDB is crystallized with the ligand. I prepared the protein for docking by removing the ligand adding necessary charges, Hydrogens etc (similarly for ligand also). X,Y,Z co-ordinates of 1st atom ( HETATM , from PDB file of cocrystallized protein) were considered for defining the binding site, with 30 grid points on each dimension and 0.500 A spacing

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