On Fri, 18 Aug 2017 at 23:46, Amani Eshtiwi <eshtiwia2017.gmail.com> wrote:
> 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
>
Dear Andy
I minimised and heated the system. Afterwards, I ran equilibration and
conventional MD production simulation. Before starting umbrella sampling I
am trying to run an equlibration simulation with QM treatment. I am using
these input parameters;
imin=0,irest=1, ntx=7, ntb=2, cut=8, ntr=0, ntc=1, ntf=1, igb=0, ntp=1,
tempi=300, temp0=300, ntt=3, ig=-1, gamma_ln=1, nstlim=100000, dt=0.001,
ntpr,ntwx,ntwr=10, ntxo=1, ioutfm=0, ifqnt=1
/
&qmm
diag_routine=0, writepdb=1, qmmask='.1-15', qmcharge=-1, qmshake=0,
printcharges=1, qm_theory='DFTB', qmcut=8, dftb_telec=100,
>
Any ideas?
Best 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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>>
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Received on Fri Aug 18 2017 - 16:30:03 PDT
