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
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>> Learn More and Donate At:
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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 - 17:30:01 PDT
