Dear Soumendranath,
Thanks for suggestion. SCC-DFTB is not a pure QM method...that is
semi-empirical method. And more importantly that is not for the system
which I am looking for.
On Fri, Jun 13, 2014 at 2:36 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
> _______________________________________________
> 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
_______________________________________________
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Received on Fri Jun 13 2014 - 05:00:04 PDT
