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 Post subject: Matched H bonds but positive free energy
PostPosted: Sat Mar 10, 2012 12:05 pm 

Joined: Fri Mar 09, 2012 5:47 pm
Posts: 3
I have run the docking of a ligand with the receptor. The final results shows that there is good match between the docked results and already known crystal structure data. However, the free energy values are in positive (ranging between +30 to +80). As you can guess that put me bit of the dilemma. How I could justify the presence of positive free energy values in the docking simulation also showing matchable binding pattern with our empirical studies


Mushtaq Hussain


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 Post subject: Re: Matched H bonds but positive free energy
PostPosted: Sat Mar 10, 2012 11:19 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 204
Please try to increase the simulation box size, it should help.


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