Re: [AMBER] Can we study the bond breaking event through Md simulation

From: Ercig Bogac (BIOCH) <"Ercig>
Date: Fri, 24 Nov 2017 08:58:37 +0000

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> yazd─▒:
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.
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 24 2017 - 01:00:02 PST
Custom Search