Low binding energy of the ligand which left from the docking site

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Youngki You

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Mar 10, 2021, 4:31:55 AM3/10/21
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Hello, 

I have a problem on the binding energy. A ligand left from the docking site during the MD simulation. When I calculate and plot the binding energy of ligand, the ligand which left from the protein showed lower binding energy (at 1us) than the ligand at the docking site (at 0). Why it is happened and how to solve this issue?

Best, 
Youngki 

Daniel Madulu SHADRACK

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Mar 16, 2021, 3:37:52 PM3/16/21
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Hi, 
Did the ligand leave completely the pocket or it found another pocket..? There are some cases where this happen. But let's first know where did it go and bind..? Did you do also a relaxed complex scheme..? 
Daniel

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