cat <<eof > mdin
  equilibrate structure 
 &cntrl
   imin=0, 
   ntc=2, ntf=2, 
   cut=12.0, igb=2, saltcon=0.2, gbsa=1,
   ntpr=50,
   nstlim = 5000, dt=0.002,
   ntt=1, tempi=0.0, temp0=300.0, tautp=1.0,
   ntx=1, irest=0, ntb=0,
   nscm = 1000,
   ntr=1,
 &end
  keep all atoms frozen
  1.0
RES 1 108
END
END
eof
sander   -O -i mdin \
-c trx.rst  -p trx.top  -ref trx.rst -o trx.equil.out -r trx.equil.rst