On Fri, 18 Aug 2017 at 21:02, Gustavo Seabra <gustavo.seabra.gmail.com>
wrote:
> Dear Armani,
>
> What version of sander are you using? Is it the last version?
>
> There was a problem with the use of halogens parameter sets, which I
> believe was solved in the most recent update. Please take a look at the
> discussion here:
>
> http://archive.ambermd.org/201602/0069.html
>
> HTH,
> —
> Gustavo Seabra
Dear Gustavo
Thank you very much for your reply.
> I am using Amber 16 Sander 2016. Which version shall I use?
Regards
Amani
>
>
>
> > Em 18 de ago de 2017, à(s) 16:19, Goetz, Andreas <agoetz.sdsc.edu>
> escreveu:
> >
> > 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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> >>>
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Received on Fri Aug 18 2017 - 16:00:02 PDT
