Hi,
I have few docked poses of a ligand inside a metalloenzyme that I want to minimise and subsequently score using QM/MM approach. Should I do a calculation for each tautomer separately ? Since the ligand is in the QM region in which bonds can be broken and formed, I dont have to worry about considering different tautomers since the best tautomer will be generated "on the fly". Am I right ?
Discovery studio 2016 , CHARMm + DMOL3 DFT
Dear Zaid Assaf,
If I understood your question correctly you will get different conformers for each calculation.
1. If you want to see the effect of the MM part on QM part you should do each calculation separately.
2. Your "best" tautomer probably will be minimize to the closest minimum.
3. What you mean by the "best"? The lowest energy minimum or the closest geometrical configuration for the docking process?
You can also generate many different conformers using some method (Monte Carlo, semi-empirical conformational search etc like e.g. in SPARTAN program) and later take the "best" tautomers and re-optimize them with the certain QMMM level.
Hope it could be useful somehow.
All the best,
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Darek
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