Dear Amani,
In this case it is hard to say what went wrong. If you were missing DFTB parameters, there would be a corresponding error message in the output. Can you successfully run MM simulations? Please make sure that this is the case. If yes,then you can send your input files and we can have a look at what might go wrong.
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 Aug 17, 2017, at 3:20 PM, Amani Eshtiwi <eshtiwia2017.gmail.com> wrote:
>
> On Thu, 17 Aug 2017 at 20:53, Goetz, Andreas <agoetz.sdsc.edu> wrote:
>
>> Dear Amani,
>>
>> Both for Br and Zn you need to install a DFTB parameter set that supports
>> these elements. There should be a corresponding error message in the mdout
>> file.
>>
>> You can also get AmberTools 17, which supports DFTB3. The default 3ob
>> parameter set contains parameters both for Br and Zn.
>>
>> All the best,
>> Andy
>>
>> Sent from my iPhone
>>
>>> On Aug 17, 2017, at 14:32, Amani Eshtiwi <eshtiwia2017.gmail.com> wrote:
>>>
>>> Dear users
>>>
>>> I am running a QM/MM calculation using Amber16 and DFTB as the QM theory.
>>> The QM region includes a bromine atom. The calculation suspends without
>>> writing any restart files. The out file does not show any error messages.
>>> When I excluded the bromine atom from the QM region the calculation runs
>>> successfully! The same calculation with bromine ran successfully when I
>>> used PM3. Anyone encountered the same problem? Is there any special way
>> to
>>> deal with nonstandard atoms when using DFTB? I also have the same problem
>>> with my Zinc-containing protein when I include Zinc atoms in the QM
>> region.
>>> Any advice will be greatly appreciated.
>>>
>>> Sincerely
>>> Amani
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>> Dear Andy
>
>
> Thank you very much for your reply. The out file does not show any error
> messages and ends with a list of the QM atom coordinates. The calculation
> halts without any updates!
>
> Best regards
> Amani
>
>>
>
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Received on Fri Aug 18 2017 - 12:30:03 PDT
