Dear Bharat,
Which version of Amber are you using? If you use Amber16, maybe you should look at the adaptive solvent QM/MM method, described in section 10.3 (page 162) of the manual.
—
Gustavo Seabra.
> Em 29 de jun de 2016, à(s) 05:44, bharat gupta <bharat.85.monu.gmail.com> escreveu:
>
> 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 - 07:00:03 PDT
