Dear Dr. Jason
Thanks for your reply.
I am so sorry I didn't give full background about my error. It was:
Unusual nbond for O: 72268 0
Using default oxygen LCPO parameters
Unusual nbond for O: 72271 0
Using default oxygen LCPO parameters
Unit 30 Error on OPEN: inpcrd
here, I am missing the inpcrd file, where I specified -y XXX.mdcrd
what keyword should be specified where I want to read the snapshots from the trajectory, according to the manual I should use -y file.mdcrd. I used the following command:
sander.MPI -O -i QMMM-GBSA.in -o QMMM-GBSA.out -p XXX.prmtop -y XXX.mdcrd
One more point please, should I calculate the surface area? when I specified gbsa=1, I got the above warring (Using default oxygen LCPO parameters), is that normal?
Please, is there any tutorial on post-process methodology? or at least give me any hint please.
Thanks
Eliac
--- On Mon, 12/27/10, 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: Monday, December 27, 2010, 4:26 AM
> 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
>
>
> >
> > 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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> > > >
> > >
> > >
> > >
> > > --
> > > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Dec 26 2010 - 21:00:04 PST
