Dear amber users,
Thank you Andy for your answer.
I have another question about this topic.
I have already carried out a classical molecular dynamic of my system. Continuously, I want to perform a QM/MM minimization starting from one snapshot of the MD. How can I do it?
Furthermore and relate with this topic. I want to know, can I consider the TYR-O* (oxygen as a radical atom) in the QM region during the QM/MM minimization, if in my topology I have the TYR residue with -OH? If not how can I perform this situation?
Thank you in advanced for your help
Anna
________________________________
De: Dr. Andreas W. Goetz <agoetz.sdsc.edu>
Enviat el: dissabte, 30 de juliol de 2016 3:14:30
Per a: AMBER Mailing List
Tema: Re: [AMBER] Question about QM/MM
Dear Anna,
Yes, it is possible to use DFT for QM/MM calculations with AMBER using any of the supported external QM programs.
If you have not performed any QM/MM simulations before, I suggest to first use one of the built-in semiempirical QM methods. Switch to DFT with external QM programs once you have confirmed that your QM/MM setup is working as expected. Finally, keep in mind that DFT will be much slower than MM or semiempirical QM/MM.
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Project Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de<http://www.awgoetz.de>
> On Jul 29, 2016, at 6:45 AM, Anna Cebrian Prats <Anna.Cebrian.uab.cat> wrote:
>
> Dear amber users,
>
>
> I have a question about QM/MM.
>
>
> I am starting to use QM/MM package with amber16. I want to perform a QM/MM minimization of my system followed by a QM/MM simulation, using a snapshot of the MD simulation of my system already performed with amber.
>
>
> In order to do that I want to perform a DFT calculation only using AMBER with any external program. This is possible??
>
>
> Thank you in advanced for your help
>
>
> Sincerely
>
>
> Anna
>
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Received on Fri Sep 02 2016 - 02:30:02 PDT
