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!
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