### Docking -- Step 1 set PSFFILE ELIC_GABR_refine_1_autopsf.psf set PDBFILE ELIC_GABR_refine_1_autopsf.pdb set GRIDPDB cagrid.pdb set GBISON 0 set DIEL 80 set SCALING_1_4 1.0 set ITEMP 300 set FTEMP 300 set GRIDFILE setp1.dx set GSCALE 0.1 set EXTRAB {EB-extrabonds.txt EB-extrabonds-cispeptide.txt EB-extrabonds-chirality.txt} set CONSPDB 0 set FIXPDB 0 set REFINESTEP 20000 set REFS merge_unique.mtz set BFS 0 set MASK 0 set MASKRES 5 set MASKCUTOFF 5 set CRYSTPDB 0 set OUTPUTNAME EB-step1 set TS 7000000 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 } source xmdff_template.namd #BEGIN XMDFF NECESSARY FUNCTIONS if {[info exists INPUTNAME]} { exec /opt/local/bin/vmd -dispdev text -e xmdff_phenix.tcl -args $PSFFILE $INPUTNAME $GRIDFILE $REFS $BFS $MASK $CRYSTPDB $MASKRES $MASKCUTOFF > map.log } else { exec /opt/local/bin/vmd -dispdev text -e xmdff_phenix.tcl -args $PSFFILE $PDBFILE $GRIDFILE $REFS $BFS $MASK $CRYSTPDB $MASKRES $MASKCUTOFF > map.log } if {$MS != 0} { minimize $MS reinitvels $ITEMP } if {$ITEMP != $FTEMP} { set ANNEALSTEP [expr abs($FTEMP-$ITEMP)*100] run $ANNEALSTEP exec /opt/local/bin/vmd -dispdev text -e xmdff_phenix.tcl -args $PSFFILE $OUTPUTNAME $GRIDFILE $REFS $BFS $MASK $CRYSTPDB $MASKRES $MASKCUTOFF > map.log reloadGridforceGrid } for {set i 0} {$i < $TS/$REFINESTEP} {incr i} { run $REFINESTEP exec /opt/local/bin/vmd -dispdev text -e xmdff_phenix.tcl -args $PSFFILE $OUTPUTNAME $GRIDFILE $REFS $BFS $MASK $CRYSTPDB $MASKRES $MASKCUTOFF > map.log reloadGridforceGrid }