Thank you sir for giving me the detail informative response.
Best Regards.
On Fri, Nov 24, 2017 at 3:50 PM, Szymon Żaczek <szymonzaczek.gmail.com>
wrote:
> Dear Rana,
>
> bond's length fluctuations that you observe are completely normal
> during MD simulations, though it is crucial to notice that it cannot
> be anyhow facilitated with the actual electron rearrangement that
> takes place during chemical reactions. Hence, whenever you want to to
> study chemical reactions you must somehow incorporate quantum methods
> into your routine. From what you have written I assume that the only
> thing you used Gaussian so far is the derivation of force field
> parameters for your heme molecule. This is not enough to study
> chemical reactions. Basically, there are several ways to study
> chemical reactions in enzymatic systems: you can use so-called cluster
> models, in which you only consider active site residues and your
> substrates (see: doi.org/10.1007/s00775-009-0511-y) - this is probably
> the easiest way to start. Alternatively, you might use QM/MM MD
> coupled with enhanced sampling methods, such as Umbrella Sampling,
> which will allow you to incorporate dynamical fluctuations of enzyme
> and substrates into studied process, what will ensure that the
> energetics of reaction that you will obtain will be based on an
> ensemble of structures, though it's important to notice that it will
> not be based on the optimized structures. The alternative is to first
> obtain profile of reaction using Umbrella Sampling, then cut out
> several structures that will represent reactants, transition state and
> products and optimize them using QM/MM schemes, for instance using the
> one implemented in ChemShell package or ONIOM in Gaussian. This method
> though is likely to be bery time consuming and computationally
> expensive.
>
> Kind regards,
> Szymon Żaczek
>
> 2017-11-24 10:14 GMT+01:00 Rana Rehan Khalid <rrkhalid.umich.edu>:
> > Yes I already done the qm calculation of this heme histidine and NO
> system
> > by using g09 I used mcpb.py tool that provide me ff for this system then
> I
> > ran the simulation. I observe that bond length increases. Thanks for your
> > response.
> > Regards
> >
> > On Nov 24, 2017 10:59 AM, "Ercig Bogac (BIOCH)" <
> > b.ercig.maastrichtuniversity.nl> wrote:
> >
> >> Dear Rana,
> >>
> >> You can use a quantum mechanics suite to study the transition state of
> >> this reaction. I do not how feasible it is in your system but in a
> basic qm
> >> system, you only need the heme, NO and the histidine. You need a good
> >> starting structure to have your system to energetically converge closer
> to
> >> the transition state energy, than run a transition state search to
> observe
> >> the bond breaking event. By this simulation, you can also calculate the
> >> energy and at which length the bond breaks. I have used turbomole back
> then
> >> for these calculations, however the system setup and the simulations
> take
> >> serious computional time.
> >>
> >> Best regards
> >>
> >> Bogac
> >>
> >> 24 Kas 2017 08:47 tarihinde Rana Rehan Khalid <rrkhalid.umich.edu>
> yazdı:
> >> Thank you.
> >>
> >> On Nov 24, 2017 9:41 AM, "Bill Ross" <ross.cgl.ucsf.edu> wrote:
> >>
> >> > In principle you could model breaking/forming bonds using a quantum
> >> > region. I haven't done it myself.
> >> >
> >> > Bill
> >> >
> >> >
> >> > On 11/23/17 10:59 PM, Rana Rehan Khalid wrote:
> >> > > So in that case can we assume when length of bond increases that
> may be
> >> > the
> >> > > breaking point of bond. Thanks
> >> > >
> >> > > On Nov 24, 2017 8:53 AM, "Elvis Martis" <elvis.martis.bcp.edu.in>
> >> wrote:
> >> > >
> >> > >> HI,
> >> > >> Using Molecular Mechanics you cannot study bond formation or
> breaking.
> >> > >>
> >> > >> Best Regards
> >> > >> Elvis Martis
> >> > >> Mumbai, INDIA.
> >> > >>
> >> > >> ________________________________________
> >> > >> From: Rana Rehan Khalid <rrkhalid.umich.edu>
> >> > >> Sent: 24 November 2017 11:21
> >> > >> To: AMBER Mailing List
> >> > >> Subject: [AMBER] Can we study the bond breaking event through Md
> >> > simulation
> >> > >>
> >> > >> Dear Amber users
> >> > >>
> >> > >> I am working on the system such a system in which heme bonded with
> NO
> >> on
> >> > >> it's distal site while on it's proximal side it make a coordinate
> bond
> >> > with
> >> > >> histidine but we know through experimental data that when NO bind
> with
> >> > heme
> >> > >> distal site the proximal histidine heme bond break. I already ran
> the
> >> > >> simulation on the system and I observed that bond length of
> proximal
> >> > >> histidine increases but not break that bond. Kindly guide me.
> >> > >> Thank you.
> >> > >> _______________________________________________
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Received on Sat Nov 25 2017 - 05:00:03 PST
