As per current AMBER QM/MM goes I think it supports following
Support is provided for the PM3, PDDG/PM3, PM3CARB1, AM1, MNDO, and
PDDG/MNDO semi-empirical Hamiltonians as well as the self-consistent charge
density functional tight binding (SCC-DFTB) method.
Check this
http://www.ncbi.nlm.nih.gov/pubmed/18072177
On Fri, Jun 13, 2014 at 1:36 PM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> Use DFTB keyword in the qmtheory part. Check back the tutorial here
> http://ambermd.org/tutorials/advanced/tutorial2/section3.htm
>
>
> On Fri, Jun 13, 2014 at 1:34 PM, Soumendranath Bhakat <
> bhakatsoumendranath.gmail.com> wrote:
>
>> As per as my understanding goes you should make sure which residues or
>> atoms you want to traet will which level of QM parameter that you can
>> easily do using qmmask. Flag ifqnt will tell Amber that you want a QM/MM
>> run. You can download the files to check the optimized structure.Quick look
>> bu downloading the trajectory and focus on QM/MM region you treated.
>>
>>
>> On Fri, Jun 13, 2014 at 1:26 PM, Kshatresh Dutta Dubey <
>> kshatresh.gmail.com> wrote:
>>
>>> Dear Jason,
>>>
>>> I am looking for QM optimization, I know that using imin=1 will give
>>> me
>>> minimized structure but I think that it will molecular mechanically
>>> minimize the system, but what for QM optimizations? If I have to use
>>> sander for minimization then what is the use of implementation of
>>> Gaussian
>>> interface? I am curious to know that - is it possible to perform QM
>>> optimization of QM region using external QM program and sander for MM
>>> region. If yes then what should I do? Using following input (complete
>>> input, I used) does not optimize the QM region, it does single point
>>> energy
>>> calculations only, while sander does optimize MM region.
>>>
>>> *QM-MM calculations for FMN domain *
>>> *&cntrl*
>>> * imin=1, maxcyc=10,*
>>> * ntb=0,*
>>> * cut=20.,*
>>> * ifqnt=1*
>>> * /*
>>> * &qmmm*
>>> * qmmask ='.819-830,2244-2295',*
>>> * qmcharge=0,*
>>> * spin =1,*
>>> * qm_theory='EXTERN',*
>>> * qmcut=20.0*
>>> * /*
>>> * &gau*
>>> * mem = '2GB'*
>>> *! method = 'B3LYP',*
>>> *! basis = '6-31G',*
>>> * use_template =1,*
>>> * num_threads = 2*
>>> * /*
>>>
>>> Thanks and regards
>>> Kshatresh
>>>
>>>
>>>
>>> On Fri, Jun 13, 2014 at 2:01 PM, Soumendranath Bhakat <
>>> bhakatsoumendranath.gmail.com> wrote:
>>>
>>> > Use these input for minimization if you are using QM/MM. Please use
>>> sander
>>> > and sander.MPI for running
>>> >
>>> > Full_Mini.in
>>> >
>>> > Initial minimization of QMMM: solvent molecules and added ions
>>> > &cntrl
>>> > imin = 1,
>>> > maxcyc = 2500,
>>> > ncyc = 750,
>>> > ntb = 1,
>>> > ntr = 1,
>>> > cut = 12.0,
>>> > ifqnt = 1,
>>> > /
>>> > &qmmm
>>> > qmmask= '557,250,238.75,86,89,75',
>>> > qmcharge=0,
>>> > qmtheory=7, *(please suggest check once)*
>>> > qmshake=1,
>>> > qm_ewald=1,
>>> > qm_pme=1,
>>> > /
>>> >
>>> > Hold the Protein fixed
>>> > 10.0
>>> > RES 1 557
>>> >
>>> > All the best.
>>> >
>>> >
>>> > On Fri, Jun 13, 2014 at 12:54 PM, Jason Swails <jason.swails.gmail.com
>>> >
>>> > wrote:
>>> >
>>> > >
>>> > >
>>> > > > On Jun 13, 2014, at 5:50 AM, Kshatresh Dutta Dubey <
>>> > kshatresh.gmail.com>
>>> > > wrote:
>>> > > >
>>> > > > Dear Prof Monard,
>>> > > >
>>> > > > Many thanks for your quick response, still I am unable to find
>>> any
>>> > > > keyword that handles the optimizing process in sander. I went
>>> through
>>> > the
>>> > > > manual bt I was unable to find such keyword. I will deeply
>>> appreciate
>>> > you
>>> > > > if you help me to handle this process so that I can get proper QM
>>> > > > optimization.
>>> > > > Thanking you again.
>>> > >
>>> > > What you're looking for is a basic minimization. Look at the imin and
>>> > > ntmin flags.
>>> > >
>>> > > HTH,
>>> > > Jason
>>> > >
>>> > > >
>>> > > >
>>> > > >
>>> > > > On Fri, Jun 13, 2014 at 12:31 PM, Gerald Monard <
>>> > > > Gerald.Monard.univ-lorraine.fr> wrote:
>>> > > >
>>> > > >> Hi,
>>> > > >>
>>> > > >> You cannot use the Gaussian optimizer since it is sander that
>>> masters
>>> > > >> what happens to the coordinates (from a coordinate set, sander
>>> asks
>>> > > >> gaussian to compute an energy, it does not let gaussian modify
>>> them,
>>> > > >> hence the "force" keyword).
>>> > > >> You'd better use one of the optimizers available in sander (&cntrl
>>> > > >> namelist) instead.
>>> > > >>
>>> > > >> Gerald.
>>> > > >>
>>> > > >>
>>> > > >>> On 06/13/2014 11:16 AM, Kshatresh Dutta Dubey wrote:
>>> > > >>> Dear Users
>>> > > >>>
>>> > > >>> I am using Amber 14 for QM/MM calculation with Gaussian as
>>> > external
>>> > > >>> interface. I have to optimize a system containing some amino
>>> acids
>>> > and
>>> > > a
>>> > > >>> ligand in QM regions. I found that Amber automatically adds some
>>> > > keywords
>>> > > >>> in route section of Gaussian input that force Gaussian to do
>>> single
>>> > > point
>>> > > >>> calculations. For example, I used :
>>> > > >>> *&gau*
>>> > > >>> * mem = '2GB'*
>>> > > >>> *! method = 'B3LYP',*
>>> > > >>> *! basis = '6-31G',*
>>> > > >>> * use_template =1,*
>>> > > >>> * num_threads = 2*
>>> > > >>> * /*
>>> > > >>> for &gau namelist and :
>>> > > >>>
>>> > > >>> *#P OPT B3LYP/6-31G SCF=(Conver=8)*
>>> > > >>>
>>> > > >>> for template file namelist. The calculations runs fine and it
>>> shows
>>> > > >> normal
>>> > > >>> termination, but I found that it does only single point
>>> calculation
>>> > not
>>> > > >>> optimizing the structure while I have mentioned optimization in
>>> route
>>> > > >>> sections. I notice that Amber adds some additional keyword such
>>> as
>>> > > >> 'Force'
>>> > > >>> in route section which restricts Gaussian to calculate forces
>>> only. I
>>> > > >> guess
>>> > > >>> it is fine for QM-MM/MD since we need forces for dynamics, but
>>> here I
>>> > > am
>>> > > >>> interested in QM/MM optimization only. The route section
>>> modified by
>>> > > >> Amber
>>> > > >>> is :
>>> > > >>>
>>> > > >>> *#P OPT B3LYP/6-31G SCF=(Conver=8) NoSymm Force Guess=Read Charge
>>> > > Prop=*
>>> > > >>> * (Field,Read)*
>>> > > >>>
>>> > > >>> How can I disable 'Force' keyword so that I can perform proper
>>> > > >>> optimization. I will be thankful for your help.
>>> > > >>>
>>> > > >>> thanks
>>> > > >>
>>> > > >> --
>>> > > >>
>>> > > >>
>>> > >
>>> >
>>> ____________________________________________________________________________
>>> > > >>
>>> > > >> Prof. Gerald MONARD
>>> > > >> SRSMC, Université de Lorraine, CNRS
>>> > > >> Boulevard des Aiguillettes B.P. 70239
>>> > > >> F-54506 Vandoeuvre-les-Nancy, FRANCE
>>> > > >>
>>> > > >> e-mail : Gerald.Monard.univ-lorraine.fr
>>> > > >> tel. : +33 (0)383.684.381
>>> > > >> fax : +33 (0)383.684.371
>>> > > >> web : http://www.monard.info
>>> > > >>
>>> > > >>
>>> > > >>
>>> > >
>>> >
>>> ____________________________________________________________________________
>>> > > >>
>>> > > >>
>>> > > >> _______________________________________________
>>> > > >> AMBER mailing list
>>> > > >> AMBER.ambermd.org
>>> > > >> http://lists.ambermd.org/mailman/listinfo/amber
>>> > > >
>>> > > >
>>> > > >
>>> > > > --
>>> > > > With best regards
>>> > > >
>>> > >
>>> >
>>> ************************************************************************************************
>>> > > > Dr. Kshatresh Dutta Dubey
>>> > > > Post Doctoral Researcher,
>>> > > > c/o Prof Sason Shaik,
>>> > > > Hebrew University of Jerusalem, Israel
>>> > > > Jerusalem, Israel
>>> > > > _______________________________________________
>>> > > > AMBER mailing list
>>> > > > AMBER.ambermd.org
>>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>>> > >
>>> > > --
>>> > > Jason M. Swails
>>> > > BioMaPS,
>>> > > Rutgers University
>>> > > Postdoctoral Researcher
>>> > > _______________________________________________
>>> > > AMBER mailing list
>>> > > AMBER.ambermd.org
>>> > > http://lists.ambermd.org/mailman/listinfo/amber
>>> > >
>>> >
>>> >
>>> >
>>> > --
>>> > Thanks & Regards;
>>> > Soumendranath Bhakat
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >
>>>
>>>
>>>
>>> --
>>> With best regards
>>>
>>> ************************************************************************************************
>>> Dr. Kshatresh Dutta Dubey
>>> Post Doctoral Researcher,
>>> c/o Prof Sason Shaik,
>>> Hebrew University of Jerusalem, Israel
>>> Jerusalem, Israel
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> Thanks & Regards;
>> Soumendranath Bhakat
>>
>>
>
>
> --
> Thanks & Regards;
> Soumendranath Bhakat
>
>
--
Thanks & Regards;
Soumendranath Bhakat
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 13 2014 - 06:00:04 PDT
