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
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Received on Thu Aug 17 2017 - 13:00:04 PDT
