###  Docking -- Step 1
 
set PSFFILE 1ake-colores_autopsf.psf
set PDBFILE 1ake-colores_autopsf.pdb
set GRIDPDB gridpdb.pdb
set DIEL 80
set SCALING_1_4 1.0
set ITEMP 310
set FTEMP 310
set GRIDFILE target.dx
set GSCALE 0.5 ; # in real mdff simulation, 0.3 is recommended
set EXTRAB 0   ; # to use secondary structure restraints, set EXTRAB {extrabonds_ss.txt}
set CONSPDB 0
set FIXPDB  0
 
set OUTPUTNAME iMDFF-test
#gridforcelite on 
set TS 500000
set MS 200
 
set MARGIN 0
 
####################################
 
structure $PSFFILE
coordinates $PDBFILE
 
paraTypeCharmm on
parameters par_all27_prot_lipid_na.inp

if {[info exists INPUTNAME]} {
  BinVelocities $INPUTNAME.restart.vel
  BinCoordinates $INPUTNAME.restart.coor
} else {
  temperature $ITEMP
}
 
#### iMDFF section ###
IMDon		yes
IMDport		3000
IMDfreq		1
IMDwait		on
######################

source mdff_template.namd