remarks Analysis protocol set message on echo on end {*==========================================================================*} {*====================== SET FILENAMES AND VARIABLES =======================*} {*==========================================================================*} {* type of non-bonded parameters *} {* choice: "PROLSQ" "PARMALLH6" "PARALLHDG" "OPLSX" *} {* The water refinement uses the OPLSX parameters *} evaluate ( $par_nonbonded = "OPLSX" ) {* parameter file(s) *} evaluate ( $par.1 = "TOPPAR:parallhdg5.3.pro" ) evaluate ( $par.2 = "TOPPAR:parallhdg5.3.sol" ) evaluate ( $par.3 = "" ) evaluate ( $par.4 = "" ) evaluate ( $par.5 = "" ) {* solvent topology file *} evaluate ( $solvent_topology = "TOPPAR:topallhdg5.3.sol" ) {* structure file(s) *} evaluate ( $struct.1 = "STRUCTURES:1xxx.psf" ) evaluate ( $struct.2 = "" ) evaluate ( $struct.3 = "" ) evaluate ( $struct.4 = "" ) evaluate ( $struct.5 = "" ) {* input coordinate file(s) *} evaluate ( $pdb.in.file.1 = "INPUTCOORDINATES:1xxx_13.pdb" ) {* output coordinate file(s) *} evaluate ( $pdb.out.file.1 = "OUTPUTCOORDINATES:analyzed_13.pdb" ) {* input distance restraint file(s) *} evaluate ( $noe.file.1 = "TABLES:1xxx_noe.tbl" ) {* Averaging for NOE restraints *} evaluate ( $noe.ave = sum ) {* input dihedral restraint file(s) *} evaluate ( $cdih.file.1 = "TABLES:1xxx_dihe.tbl" ) {* seed for velocity generation *} evaluate ( $seed = 1234123 ) {* set number of md steps for the heating stage *} evaluate ( $mdsteps.heat = 20 ) {* set number of md steps for the hot md stage *} evaluate ( $mdsteps.hot = 100 ) {* set number of md steps for the cooling stage *} evaluate ( $mdsteps.cool = 20 ) {* seed for velocity generation *} evaluate ( $seed = 1234123 ) {* set acceptance criteria *} evaluate ( $accept.noe = 0.50 ) evaluate ( $accept.cdih = 5.00 ) evaluate ( $accept.coup = 1.00 ) evaluate ( $accept.sani = 0.00 ) evaluate ( $accept.vean = 5.00 ) {*==========================================================================*} {*=========== READ THE STRUCTURE, TOPOLOGY AND PARAMETER FILES =============*} {*==========================================================================*} structure @$struct.1 end topology @$solvent_topology end parameter @$par.1 @$par.2 end {*==========================================================================*} {*================== SET VALUES FOR NONBONDED PARAMETERS ===================*} {*==========================================================================*} parameter nbonds nbxmod=5 atom cdiel shift cutnb=9.5 ctofnb=8.5 ctonnb=6.5 eps=1.0 e14fac=0.4 inhibit 0.25 wmin=0.5 tolerance 0.5 end end {*==========================================================================*} {*========================= READ THE COORDINATES ===========================*} {*==========================================================================*} coor @@$pdb.in.file.1 {*==========================================================================*} {*========================= READ THE EXPERIMENTAL DATA =====================*} {*==========================================================================*} noe reset nrestraints = 10000 ceiling = 100 @$noe.file.1 averaging * $noe.ave potential * soft scale * 50 sqconstant * 1.0 sqexponent * 2 soexponent * 1 rswitch * 1.0 sqoffset * 0.0 asymptote * 2.0 end restraints dihedral reset @$cdih.file.1 scale = 200 end {*==========================================================================*} {*============================ SET FLAGS ===================================*} {*==========================================================================*} flags exclude * include bond angle dihe impr vdw elec noe cdih coup oneb carb ncs dani vean sani prot harm end constraints interaction (not resname ANI) (not resname ANI) weights * 1 dihed 5 end interaction ( resname ANI) ( resname ANI) weights * 1 end end {*==========================================================================*} {*======================= CHECK RESTRAINT VIOLATIONS =======================*} {*==========================================================================*} evaluate ($accept = 0) print threshold=$accept.noe noe evaluate ($v_noe = $violations) print threshold=0.5 noe evaluate ($v_noe_0.5 = $violations) print threshold=0.4 noe evaluate ($v_noe_0.4 = $violations) print threshold=0.3 noe evaluate ($v_noe_0.3 = $violations) print threshold=0.2 noe evaluate ($v_noe_0.2 = $violations) print threshold=0.1 noe evaluate ($v_noe_0.1 = $violations) evaluate ($rms_noe = $result) print threshold=$accept.cdih cdih evaluate ($rms_cdih=$result) evaluate ($v_cdih = $violations) coupl print thres = $accept.coup class c1 end evaluate ($rms_coup = $result) evaluate ($v_coup = $violations) sani print threshold = $accept.sani class rdc1 end evaluate ($rms_sani = $result) evaluate ($v_sani = $violations) vean print threshold = $accept.vean class vea1 end evaluate( $rms_vean = $result) evaluate( $v_vean = $violations) if ($v_noe > 0) then evaluate ( $accept=$accept + 1 ) end if if ($v_cdih > 0) then evaluate ( $accept=$accept + 1 ) end if if ($v_coup > 0) then evaluate ( $accept=$accept + 1 ) end if if ($v_sani > 0) then evaluate ( $accept=$accept + 1 ) end if if ($v_vean > 0) then evaluate ( $accept=$accept + 1 ) end if if ($accept = 0 ) then evaluate ( $label = "ACCEPTED" ) else evaluate ( $label = "NOT ACCEPTED" ) end if {*==========================================================================*} {*================ COMPUTE RMS DIFFERENCE BETWEEN OBSERVED =================*} {*========================= AND MODEL DISTANCES. ===========================*} {*==========================================================================*} constraints interaction (not resname TIP* and not resname ANI) (not resname TIP* and not resname ANI) end print thres=0.05 bonds evaluate ($rms_bonds=$result) print thres=5. angles evaluate ($rms_angles=$result) print thres=5. impropers evaluate ($rms_impropers=$result) energy end remarks Structure $label remarks E-overall: $ener remarks E-NOE_restraints: $noe remarks E-CDIH_restraints: $cdih remarks E-COUP_restraints: $coup remarks E-SANI_restraints: $sani remarks E-VEAN_restraints: $vean remarks RMS-NOE_restraints: $rms_noe remarks RMS-CDIH_restraints: $rms_cdih remarks RMS-COUP_restraints: $rms_coup remarks RMS-SANI_restraints: $rms_sani remarks RMS-VEAN_restraints: $rms_vean remarks NOE Acceptance criterium: $accept.noe remarks NOE violations > $accept.noe: $v_noe remarks All NOE viol. (>0.5,0.4,0.3,0.2,0.1A): $v_noe_0.5 $v_noe_0.4 $v_noe_0.3 $v_noe_0.2 $v_noe_0.1 remarks CDIH Acceptance criterium: $accept.cdih remarks CDIH violations > $accept.cdih: $v_cdih remarks COUP Acceptance criterium: $accept.coup remarks COUP violations > $accept.coup: $v_coup remarks SANI Acceptance criterium: $accept.sani remarks SANI violations > $accept.sani: $v_sani remarks VEAN Acceptance criterium: $accept.vean remarks VEAN violations > $accept.vean: $v_vean write coordinates sele= (not resn TIP3) output =$pdb.out.file.1 end stop