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,
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,
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
Received on Sun Dec 26 2010 - 10:00:04 PST
