Dear Andy
After installing the halogen and zinc parameter sets, the DFTB calculation
runs with the isolated ligand but not with the protein-ligand complex
despite the use of the same input parameters which I sent to you.
Do you think the problem is arising from zinc ions present in the active
site?
Regards
Amani
On Sat, 19 Aug 2017 at 00:26, Amani Eshtiwi <eshtiwia2017.gmail.com> wrote:
> 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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Received on Fri Aug 18 2017 - 17:00:02 PDT
