Mr Justin:

I have tried to do energy minimization in this situation which only existing 
small molecule in water, I found  the structure of organic molecule didn’t 
become distortions. I think  the distortions of organic molecules are due to 
these stronger interactions between small molecules and enzyme, because there 
is a enzyme molecule in the previous simulation. Do you think this 
consideration is correct? In the case, do you think this phenomenon  is normal? 
What’s more, I checked out the top file of small molecules and don’t find error 
and include the information of improper dihedrals.

Thank you very much!

Yujie liu
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