Here you can find an example of an input for running QM/MM using sander but treating the QM part with Gaussian. This procedure will allow you to increase the level of theory for the treatment of the QM part (and thereby, the computational cost :)).
QM/MM input calling Gaussian as external program
&cntrl
ntx = 5, irest = 1, ntrx = 1,
ntxo = 1, nmropt = 1,
ntpr = 100, ntwx =100,
ntf = 1, ntb = 2, dielc = 1.0,
cut = 12., nsnb = 10,
imin = 0, ibelly = 0, iwrap = 1,
nstlim = 200, dt = 0.0005,
temp0 = 300.0, tempi = 300.0,
ntt = 1, vlimit = 20.0,
ntp = 1,
ntc = 1, tol = 0.00001, pres0=1, comp=44.6,
jfastw=0, nscm=1000,
ifqnt=1,
/
&qmmm
iqmatoms=178,179,180,181,182,183,184,185,186,187,188,189,
196,197,198,199,200,201,
1876,1877,1878,1879,1880,1881,1882,1883,
1939,1940,1941,1942,1943,1944,1945,1946,
1979,1980,1981,1982,1983,1984,1985,1986,1987,1988,1989,1990,
2774,2775,2776,2777,2778,2779,2780,2781,
3377,3378,3379,3380,3381,3382,3383,3384,3385,3386,3387,3388,3389,3390,3391,3392,
3420,
6787,6788,6789,
6790,6791,6792,
qm_theory='EXTERN',
qm_ewald=0,
qmcharge=-1,
spin=1,
writepdb= 1,
/
&gau
method='B3LYP',
basis='6-311+G(2d,2p)',
num_threads=8,
NOTE: in case you need to specify special parameters (e.g. Zn2+ for DFT methods), activates the flag as use_template=1 and incorporate those parameters in a file called gau_job.tpl placed in the same folder were you are going to run your calculations.
&end
/
&wt
type='DUMPFREQ', istep1=5,
&end
&wt
type=“END”,
&end
/
ncsu_smd
output_file = 'extern.dat
output_freq = 10
variable
type = DISTANCE
i = (187,3377)
path = (x,1.00)
harm = (1000.0)
end variable
variable
type = LCOD
i = (3381,3378,3378,186)
r = (1.0,-1.0)
path = (-1.9,1.9)
harm = (1000.0)
end variable
~
