Yes, it is correct that Amber supports all above methods, but in current
implementation, amber 14, it also supports external interfaces.
You may check this..
http://onlinelibrary.wiley.com/doi/10.1002/jcc.23444/abstract
On Fri, Jun 13, 2014 at 2:42 PM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> 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
>
--
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 - 07:30:01 PDT
