Equillibrating the system
 &cntrl
  imin   = 0,
  irest  = 0,
  ntx    = 1,
  ntb    = 1,
  cut    = 10,
  ntr    = 1,
  ntc    = 2,
  ntf    = 2,
  tempi  = 300.0,
  temp0  = 300.0,
  ntt    = 3,
  gamma_ln = 1.0,
  nstlim = 50000, dt = 0.002
  ntpr = 500, ntwx = 1000, ntwr = 1000
 /
Keep protein + DNA + CTP + MG fixed with weak restraints
50.0
RES 1 395
END
END