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 Fri Nov 24 2017 - 03:00:02 PST
