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
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>
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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 - 15:30:02 PST
