On Sun, Dec 26, 2010 at 7:42 PM, Eliac Brown <eliacbrown.yahoo.com> wrote:
> Dear Dr. Markus and Dr. Jason
> Thanks for both of you for replying.
> Indeed, this is the first time for me to run this type of calculation, so
> bear with me, please.
> In GBSA, surface area should be calculated, shouldn't it?
> where, gbsa = 0 asks for no computation of the surface area.
> For QM/MM-GBSA calculation, there are two ways to run it:
> 1- To extract the snapshots using ptraj and then to run minimization of
> each structure using imin=1,maxcyc=0
>
maxcyc = 0 and maxcyc = 1 are the same, I think.
> 2- To use imin = 5 and maxcyc = 1 on the trajactory.
> I tried the 2nd way, but the job killed without any error:
>
You'll have to explain this more. What do you mean "without any error"? Did
you get any messages?
Good luck!
Jason
sander.MPI -O -i QMMM-GBSA.in -o QMMM-GBSA.out -p XXX.prmtop -y XXX.mdcrd
>
> Is there any tutorial on post-process methodology? or at least give me any
> hint please.
>
> Thanks and sorry for my naive question
> Merry xmas
> Eliac
>
> --- On Sun, 12/26/10, Jason Swails <jason.swails.gmail.com> wrote:
>
> > From: Jason Swails <jason.swails.gmail.com>
> > Subject: Re: [AMBER] QM/MM-MD binding energy
> > To: "AMBER Mailing List" <amber.ambermd.org>
> > Date: Sunday, December 26, 2010, 11:06 PM
> > A couple comments below:
> >
> > On Sun, Dec 26, 2010 at 10:46 AM, Markus Kaukonen <
> markus.kaukonen.iki.fi>wrote:
> >
> > > Dear Eliac,
> > > Basically you should go through tutorial 3
> > > http://ambermd.org/tutorials/advanced/tutorial3/
> > >
> > > You run MD, generate snapshots for ligand, protein and
> > complex for
> > > subsequent QM/MM-GBSA runs
> > > and most often strip all water.
> > >
> > > Below is an example for an input file for sander for a
> > system, with NO
> > > guarantee whatsoever (read the manual)
> > > for QM/MM-GBSA energy (change at least indexes for QM
> > atoms and
> > > possibly QM charge)
> > >
> > > QM/MM GBSA, Complex
> > > &cntrl
> > > irest=0,ntx=1,
> > > imin=1,maxcyc=0,drms=0.0001,
> > >
> >
> > If you set imin = 5 and maxcyc = 1, then you will get the
> > single point
> > energies for every snapshot of a trajectory. You will
> > have to post-process
> > the output file yourself, since neither MM/PBSA program is
> > equipped to parse
> > a QM/MM mdout file.
> >
> >
> > > ntpr=1,ntwx=0,ntwv=0,ntwe=1,
> > > ntf = 1, ntb = 0,
> > > igb = 5, dielc = 1.0,
> > > cut = 1000.0, nsnb = 10,
> > > scnb = 2.0, scee = 1.2,
> > >
> >
> > If you are using Amber 11, scnb and scee have been removed
> > as namelist
> > options (they're in the prmtop now)
> >
> > All the best,
> > Jason
> >
> > intdiel= 1.0, extdiel=80.0,
> > > rgbmax = 1000.0, gbsa = 0,
> > > ifqnt=1
> > > &end
> > > &qmmm
> > > qmmask=".11092-11095,12467-12549"
> > ! (QM region)
> > > qmcharge=0,
> > !(Charge on QM region)
> > > qm_theory="DFTB",
> > !(Use the DFTB semi-empirical Hamiltonian)
> > > qmcut=1000.0,
> > !(Use1000 angstrom
> > cut off for QM region)
> > > printcharges=1,
> > !print QM charges
> > > dftb_telec=100.0
> > !temperature for fermi func.
> > > &end
> > >
> > >
> > >
> > > Hope this helps, Markus
> > >
> > >
> > >
> > > --
> > > --www=http://www.iki.fi/markus.kaukonen
> > > --Markus.Kaukonen.iki.fi
> > > --office: N102 Nano building FIN-02015 TKK
> > > --home: Viinirinne 3 F 12, 02630 Espoo, FIN
> > > --tel: h 045-1242068, w 4518694, 050-5112785
> > > --Rikos ei kannata, eika maatalous
> > > --Suomessa. (Paimio 1998) ---
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Dec 26 2010 - 20:30:04 PST
