minimize the system
 &cntrl
  imin=1, maxcyc=5000, ncyc=2500,
  cut=9.0, ntb=1,
  ntc=1, ntf=1,
  ntpr=10,
  ntr=1,
  restraintmask=':1-768',
  restraint_wt=2.0,
  ifqnt=1
 /
 &qmmm
  iqmatoms=3308,3309,3310,3311,3312,3313,3314,3315,3316,3317,11973,11974,11975,11976,11977,11978,11979,11980,11981,11982,11983,11984,11985,11986,11987,11988,11989,11990,11991,11992,11993,11994,11995,11996,11997,11998,11999,12000,12001,12002,12003,12004,12005,12006,12007,12008,12009,12010,12011,12012,
  qmcharge=-1,
  qmtheory=1,
  qmshake=0,
  qm_ewald=1, qm_pme=1,
  writepdb=1
 /