Dear Soumendranath,
Thanks for your help but that is for semi-empirical QM theory, I am
interested in DFT theory using external interface ( gaussian).
On Fri, Jun 13, 2014 at 2:26 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
>
>
>
--
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 - 05:00:02 PDT
