Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface

From: Kshatresh Dutta Dubey <kshatresh.gmail.com>
Date: Fri, 13 Jun 2014 17:58:59 +0300

Dear Prof Monard,
   Thanks for your detailed explanation, it is really helpful. However, I
have still some queries. QM/MM run using Gaussian is producing some file,
like old.gau_job.log, old.gau_job.inp and others. When I am checking
*old.gau_job.log
*file there is no proper convergence informations as usually we find in any
Gaussian optimized output file. Indeed it successfully finishes proper
termination in less than 1 hour while number of atoms are more than 100.
When I ran same old.gau_job.inp file by remove 'Force' keyword appended by
sander, it runs as usual QM optimizations and prints all convergence
informations and takes relatively very long time in proper convergence (
same input without 'Force' keyword on same machine). Therefore, I guess
that even assigning min=1 keyword, Gaussian is not optimizing the system
and only computing its energy (as single point calculations).
    I am attaching old.gau_job.inp as well as QM-MM.in. I request you to
tell me where am I doing a mistake. I will be thankful for your help.

With Regards
Kshatresh



On Fri, Jun 13, 2014 at 4:48 PM, Gerald Monard <
Gerald.Monard.univ-lorraine.fr> wrote:

> Hi,
>
> On 06/13/2014 01:26 PM, Kshatresh Dutta Dubey 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?
>
> No. imin=1 will minimize the _whole_ system: QM _+_ MM, except if you
> use some kind of restraints (ibelly, which is not recommended for
> minimization).
> Minimization means "energy minimization": you compute the energy of the
> _whole_ system (QM + MM and their interactions), the gradient, and from
> the latter, the minimization algorithm decide how to modify the
> coordinates of the whole system to obtain a new set of coordinates that
> should lead to a lower energy.
> That is to say: to perform minimization, the algorithm must have
> information on the whole system, not part of it.
>
> If you refer to some kind of minimization algorithm as develop in the
> group of Weitao Yang some years ago or in the group of Keiji Morokuma
> (iterative minimization, J. Chem. Phys. 112, 3483--3492 (2000) or J.
> Comp. Chem., 24, 760-769 (2003)), this is not implemented in Amber.
>
>
> > 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.
>
> In the input below, both regions are optimized at the same time (as
> there is only 1 energy computed: a QM/MM energy).
>
> Gerald.
>
>
> >
> > *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
> >>
> >
> >
> >
>
> --
>
> ____________________________________________________________________________
>
> 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




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Received on Fri Jun 13 2014 - 08:30:02 PDT
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