On Fri, 18 Aug 2017 at 23:37, Amani Eshtiwi <eshtiwia2017.gmail.com> wrote:
> 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
>> >Dear Andy
>
>
I have downloaded the specific purpose DFTB parameter setes for halogens
and zinc. The parameter files were found and they appeared in the out file.
However, the calculation is still suspending without writing any restart
files or error messages. The last word appearing in the out file was
Results. MM calculations as well as Amber/PM3 calculations run without any
problems on the same system.
I will send you my input parameters.
Thanks.
Kind regards
Amani
>> > —
>> > 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 - 16:00:03 PDT
