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