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
_______________________________________________
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Received on Fri Jun 13 2014 - 04:30:02 PDT
