Dear Andy
Thank you very much. I will try that as you suggested.
Regards.
Sadaf
On Sat, Mar 28, 2020 at 12:23 AM Goetz, Andreas <agoetz.sdsc.edu> wrote:
> Hi Sadaf,
>
> Amber will use Orca as an external QM program if you have Orca installed.
> See chapter 10.2 of the Amber 19 manual. As a reference please have a look
> at following publication where we introduce the interface to external QM
> programs for QM/MM simulations:
>
> https://dx.doi.org/10.1002/jcc.23444
>
> If you are not familiar with QM/MM simulations, I would suggest to get
> started with semiempirical or DFTB methods. These are built into Amber and
> computationally cheap so you don’t have to waste a lot of computational
> resources while running tests. There is a very basic QM/MM example in the
> Amber tutorials here
>
> http://ambermd.org/tutorials/
>
> To study a reaction, you probably will want to combine a QM/MM potential
> with an appropriate sampling method to find a reaction path, e.g. nudged
> elastic band or umbrella sampling along a suitable reaction coordinate.
>
> All the best,
> Andy
>
> —
> Dr. Andreas W. Goetz
> Assistant Research Scientist
> San Diego Supercomputer Center
> Tel: +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web: www.awgoetz.de
>
> > On Mar 27, 2020, at 4:39 PM, Sadaf Rani <sadafrani6.gmail.com> wrote:
> >
> > Dear Jim
> > Thank you very much for your reply. I have a little confusion that how
> will
> > I integrate both Orca and Amber to run parallel for doing hybrid QM/MM?
> > Looking forward to hearing from you.
> >
> > Thanks.
> >
> > Sadaf
> >
> > On Fri, Mar 27, 2020 at 6:57 PM James Kress <jimkress_58.kressworks.org>
> > wrote:
> >
> >> ORCA is my preferred QM software for use with Amber. You can get it
> here:
> >>
> >> https://orcaforum.kofo.mpg.de/index.php
> >>
> >> It is free for academics.
> >>
> >> Jim
> >>
> >> James Kress Ph.D., President
> >> The KressWorksR Institute
> >> An IRS Approved 501 (c)(3) Charitable, Nonprofit Corporation
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> >> -----Original Message-----
> >> From: Sadaf Rani <sadafrani6.gmail.com>
> >> Sent: Friday, March 27, 2020 5:37 AM
> >> To: AMBER Mailing List <amber.ambermd.org>
> >> Subject: [AMBER] How to setup a QM/MM calculation in Amber
> >>
> >> Dear Amber users
> >> I want to find out the reaction mechanism of an enzyme by QM/MM method.
> I
> >> need your suggestions on how to set up the system. Which QM software
> should
> >> I couple with Amber and how? Could you please suggest me some
> literature on
> >> it? I am new to this and will be doing it for the first time. Any of
> your
> >> suggestions will really help me.
> >>
> >> Thanks in advance.
> >>
> >> Sadaf
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Received on Fri Mar 27 2020 - 18:00:02 PDT
