120
ntr=1, Obtain a restart file
/
Keep complex fixed
500.0 Positional restraints for the solute
(residues 1 to 15 of 2-HP-β-CD)
RES 1 15
END
END
Min2.in
Minimization of system keeping complex fixed
&cntrl
imin=1, maxcyc=5000, ncyc=5000,
cut=10.0, ntb=1, ntr=1,
/
Keep complex fixed
10.0
RES 1 15
END
END
Min3.in
Minimization of system with complex unrestrained
&cntrl
imin=1, maxcyc=10000, ncyc=5000,
cut=10.0, ntb=1, ntr=0,
/
Note: The input files demonstrate the basic commands of
each procedure and they should be merely considered as simplified examples. The command choices and their values may vary
and depend on the particular system under study. Also, for simplicity, some less important keywords were omitted.
4. Input file for complex heating with AMBER:
Heat.in
Equilibration with restraints on complex
&cntrl
imin=0, irest=0,
cut=10.0, ntb=1, ntr=1,
ntc=2, ntf=2, SHAKE algorithm applied
tempi=0, temp0=310.0, Target temperature
ntt=3, Langevin thermostat
gamma_ln=2.0, Collision frequency
nstlim=200000, # of MD steps
dt=0.002, time-step
/
Georgios Leonis et al.