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
2- To use imin = 5 and maxcyc = 1 on the trajactory.
I tried the 2nd way, but the job killed without any error:
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) ---
> >
> > _______________________________________________
> > AMBER mailing list
> > 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
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Received on Sun Dec 26 2010 - 19:00:04 PST
