* Generate PSF and CHARMM coordinate set for * Human phospholipid scramblase 1 * set name "helix_allh" set output mini_@name ! this is the output : replace by any other complexe name ! ! Read in Topology and Parameter files !_____________________________________ open unit 1 card read name "../lib/toph19_eef1.1.inp" read RTF card unit 1 close unit 1 open unit 1 card read name "../lib/param19_eef1.1.inp" read PARA card unit 1 close unit 1 ! Read in structure and psf file of the Bovine alpha lactalbumine 1f6r !_____________________________________________________________________ open read unit 9 card name ../lib/@name.psf read psf card unit 9 close unit 9 open read unit 10 card name ../coor/@name.crd read coor card unit 10 close unit 10 ! write the pdb coordinates (+hydrogens) in the comp set !coor copy comp ! Specify non bonded interactions and fast energy routines !faster 5 NBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 5/08/91, suggested cutoff scheme energy ! some useful protein selection definitions ! to see stream ../lib/prot.def !rms difference between initial and minimized structures open unit 11 write form name ../out/@output.rms write title unit 11 *# JOBNAME: @output *# RMS Coordinate deviations with minimization step no. *# STEP prot pept water trace * close unit 11 !Energy variations during minimization open unit 12 write form name ../out/@output.enr write title unit 12 *# JOBNAME: @output *# Energy contributions with minimization step no. *# GRMS and ENER are calculated w/out harmonic restraints * !*# STEP ENER ELEC VDW BOND ANGL DIHE IMPR UREY USER close unit 12 !===================================================== ! Specify energy minimization inside command loop !===================================================== set 1 0 ! loop index (step count) set 2 500 ! step increment (no. of minimization sd steps each pass) set 7 100 ! step increment (no. of minimization conj steps each pass) set 8 600 ! total nb of min. steps set 3 12000 ! step limit set 4 800 ! coordinate dump frequency. set 5 0 ! coordinate dump counter. set 6 5 ! nprint ! Initialize harmonic constraint potential. ! cons harm : hold atoms in place , Exponentiel harmonic constraints CONS HARM EXPOnent 2 FORCe 1 ! { very tight on backbone of pcna } SCALar CONSTraint SET 250. SELEct ( prot .AND. main ) END ! { quite tight on sidechains of pcna } SCALar CONSTraint SET 200. SELEct ( prot .AND. side ) END !SCALar CONSTraint SET 50. SELEct ( resname TIP3 ) END !SCALar CONSTraint SET 25. SELEct (side ) END ! to check SCAlar CONSTraint SHOW !stop ! OK !do @2 steps of steepest descent with constraints label mini !read the coordinate to the comp set open read unit 10 card name ../coor/@name.crd read coor comp card unit 10 close unit 10 FORMAT minimize sd nstep @2 nprint @6 - ihbfrq 0 inbfrq 10 tolgrd 0.01 minimize conj nstep @7 nprint 5 - inbfrq 10 tolgrd 0.01 incr 1 by @8 incr 5 by @8 !{reduce the harmonic force constants} SCALar CONStraint MULTiply 0.65 ! check the magnitude of the harmonic force SCALar CONStraint SHOW FORMAT (F7.4) ! protein structural changes. ! prot only coor orie rms sele ( prot ) end set a ?RMS ! trace only coor orie rms sele ( trace ) end set a @a ?RMS !write the set of rms difference to output open unit 11 appe form name ../out/@output.rms write title unit 11 *@1 @a * close unit 11 FORMAT (F8.2) ! keep track of the current restraint energy. set h ?HARM ! get an energy w/out the restraints SKIPE HARM GETE ! switch on restraints again SKIPE EXCL ALL !get total energy w/o restraints set b ?ENER ! get EXTernal energy contributions. set c ?ELEC incr c by ?VDW incr c by ?USER ! get INTernal energy contributions. set d ?BOND incr d by ?ANGL incr d by ?DIHE incr d by ?IMPR incr d by ?UREY !write out the resulting energy differences open unit 12 appe form name ../out/@output.enr write title unit 12 *STEP= @1 ENER= @b GRMS= ?GRMS ELEC= ?ELEC VDW= ?VDW *EXTERNAL= @c INTERNAL= @d USER= ?USER HARM= @h *BOND= ?BOND ANGL= ?ANGL DIHE= ?DIHE IMPR= ?IMPR UREY= ?UREY * close unit 12 FORMAT !check if the coordinates are written now or later if 5 lt @4 goto mini open unit 1 card write name ../pdb/@output_@1.pdb FORMAT (F8.2) write coor pdb unit 1 * Minimization of Human phospholipid scramblase 1 * JOBNAME: @output : Minimization step= @1 *=========================================================== * ENERGIES: *STEP= @1 ENER= @b GRMS= ?GRMS ELEC= ?ELEC VDW= ?VDW *EXTERNAL= @c INTERNAL= @d USER= ?USER HARM= @h *BOND= ?BOND ANGL= ?ANGL DIHE= ?DIHE IMPR= ?IMPR UREY= ?UREY * close unit 12 FORMAT !check if the coordinates are written now or later if 5 lt @4 goto mini open unit 1 card write name ../crd/@output_@1.crd FORMAT (F8.2) write coor pdb unit 1 * Minimization of Human phospholipid scramblase 1 * JOBNAME: @output : Minimization step= @1 *=========================================================== * ENERGIES: *STEP= @1 ENER= @b GRMS= ?GRMS ELEC= ?ELEC VDW= ?VDW *EXTERNAL= @c INTERNAL= @d USER= ?USER HARM= @h *BOND= ?BOND ANGL= ?ANGL DIHE= ?DIHE IMPR= ?IMPR UREY= ?UREY *=========================================================== * RMS Coordinate deviations: * STEP prot .or. pept prot pept water trace * @1 @a *=========================================================== * Human scramblase 1 : all-atom topology/parameters * Initial Coordinates: * set 5 0 ! reset coordinate dump counter if 1 lt @3 goto mini ! now do a minimization without any constraint cons harm clear ! check that constraint==0 scalar cons show !write the structure after mini with constraints open unit 1 card write name ../coor/@output_intermediate.pdb write coor pdb unit 1 ! 2000 conj grad. ! pour finir en beaute minimize conj nstep 2000 nprint 100 tolgrd 0.001 - inbfrq 10 minimize conj nstep 2000 nprint 100 tolgrd 0.001 - inbfrq 10 open unit 18 card write name ../coor/@output_final.pdb write coor pdb unit 18 open unit 19 card write name ../coor/@output_final.crd write coor card unit 19 * Human phospholipid scramblase 1 from human_plscr1_B99990001.pdb * close unit 19 FORMAT (F7.4) ! protein structural changes. ! prot only coor orie rms sele ( prot ) end set a ?RMS set a @a ?RMS ! trace only coor orie rms sele ( trace ) end set a @a ?RMS !main chain - to compare with back !coor rms sele ( resname TIP3 ) end !set a @a ?RMS !write the set of rms difference to output open unit 11 appe form name ../out/@output.rms write title unit 11 *@1 @a * close unit 11 stop ! phew