Hi Anna
A couple of things here. First, the internal semiempirical methods
within amber do not handle radicals species. In your case, the Tyr-O^.
which is a doublet. So, you need to use the external programs for your QM.
As you for your classical MD, the setup you have now does not work. You
have an 'extra' atom in your crd/prmtop, since you built it with a Tyr-OH
To make this work, you need to create a Tyr-O^. radical and rebuild your
system in tleap. There might be tricks you can do using parmed to delete
an atom.
Of importance here is the fact that, once you start doing QM/MM, the
classical parameters for the QM part are NEVER used, except the vdw
data. This means that the classical parameters are irrelevant, and can
be guessed, since they are not used. However, if you want to run some
classical MD first and THEN move to QM/MM, your MM parameters for this
new residues mist be at least reasonable.
Adrian
On 9/2/16 3:01 AM, Anna Cebrian Prats wrote:
> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Fri Sep 02 2016 - 08:30:03 PDT
