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

From: Rana Rehan Khalid <rrkhalid.umich.edu>
Date: Fri, 24 Nov 2017 14:14:01 +0500

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> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 24 2017 - 01:30:02 PST
Custom Search