Hello,
My comments are below
On Sun, Dec 26, 2010 at 9:51 PM, Eliac Brown <eliacbrown.yahoo.com> wrote:
> 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
>
This file is still required -- I missed that you omitted that on the last
email. You're required to provide an inpcrd file, but it is just a dummy
file that doesn't serve any purpose (except to provide box information for
periodic simulations).
Good luck!
Jason
> 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
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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
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Received on Sun Dec 26 2010 - 21:30:04 PST
