AMBER Archive (2006)

Subject: AMBER: For different ligand conformation

From: pkb bioinfo (pkstruct_at_gmail.com)
Date: Mon Jul 31 2006 - 08:53:45 CDT

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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