Dear Amber Users,
Thank you again David for the advice on setting the initial system. I am
able to run the QM/MM minimization now. But I have a few more questions
about my study, which I have stated below.
I am studying a simultaneous proton transfer, nucleophilic attack (by water
molecule), bond breakage using QM/MM approach [in short single step
inversion mechanism in Glycoside Hydrolase]. For this, I performed a
classical MD simulation and selected the lowest energy structure for QM/MM
calculation. Since I was not knowing which water molecule to consider for
the reaction to take place, I, therefore selected the lowest energy
structure and water molecules with in 3 Ang of the Acid residue, I included
in the QM/MM calculation. My QM region includes 2 acid residues, 1 base and
3 water molecules. I want to know whether selecting starting structure in
this manner for Q
M/MM reaction (especially with regard to the choice of water molecule) is
correct or not??
My QM/MM protocol is as follows:
1. Minimization
2. Gradual heating with restraints of protein + ligand for 50 ps
3. Unrestrained NPT Equilibration 50 ps
4. Production run in NPT ensemble 300 ps.
Do I expect to see the reaction taking place during the 4th step i.e.
production run ? I have read that for the free energy profile for the
reaction, I need to perform Umbrella Sampling, but I need to be sure
whether I should first confirm whether the reaction is taking place during
the production run or not? Am I going in the right direction?
--
*Best Regards*
Bharat
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Received on Wed Jun 29 2016 - 02:00:03 PDT
