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
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Received on Fri Jun 13 2014 - 05:00:02 PDT
