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
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 13 2014 - 05:00:03 PDT
