Dear AMBER users,
I am simulating a ligand in the protein.Experimentally it has been proven
that the ligand stays in the active site
in two different conformation and the catalysis give two different products.
I did docking in Autodock3 and hoped during simulation two different
conformation will be apparent.
>From the simulation one conformation is somwhow clear but the other
conformation is not visible.
So please guide me any procedure in which I will be able increase the
flexibility of the ligand and I will be able to see
the other conformation.These are the follwing AMBER input files for
periodic boundary simulation.
Initial mnimisation with cartesian restraints on solute
&cntrl
imin=1,maxcyc=200,
ntpr=5,
ntr=1,
&end
Group input for restarined atoms
100.0
RES 1 500
END
END
Minimization of the entire molecule
&cntrl
imin=1,maxcyc=200,
ntpr=5,
&end
Heating up the system equilibration stage 1
&cntrl
nstlim=5000, dt=0.002, ntx=1, irest=0, ntpr=500, ntwr=5000, ntwx=5000,
tempi =100.0, temp0=300.0, ntt=1, tautp=2.0, ig=209858,
ntb=1, ntp=0,
ntc=2, ntf=2,
nrespa=2,
&end
Constant pressure constant temperature equilibration stage 2
&cntrl
nstlim=500000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=500, ntwx=500,
temp0=300.0, ntt=1, tautp=2.0,
ntb=2, ntp=1, ntc=2, ntf=2,
nrespa=1,
&end
Thanking you in advance
Regards
Pravas
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Received on Wed Aug 02 2006 - 06:07:07 PDT
