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
> > _______________________________________________
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> > 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 Thu Aug 17 2017 - 13:30:02 PDT
