Sun Oct 9 22:57:07 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 22:57:07 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4305 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5025197 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -21.94100 31.48900 ymin,ymax (A): -88.03900 -17.19600 zmin,zma (A): -64.11700 -0.2750000 x,y,z range (A): 53.43000 70.84300 63.84200 scale (grids/A): 0.5025197 object centre (A): 4.774000 -52.61750 -32.19600 number of atom coordinates read : 4305 total number of charged atoms : 4145 net assigned charge : 2.000011 assigned positive charge : 648.7268 centred at (gu) : 89.50680 89.14563 91.78867 assigned negative charge : -646.7314 centred at (gu) : 89.61654 89.16082 91.84204 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7116 nv = 96 ne = 84 npr = 83673 no. pairs analyzed = 83673 no. exposed pairs = 5801 no. arc points = 41189 no. surface atoms = 1928 nbur = 2377 mkacc time = 0.2900000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.736000 m= 247 mr = 3496 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 3858 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3967 ## 607 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 9528 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6661898E-11 -1.1223439E-10 midg,1,midg; midg,igrid,midg 5.6746437E-11 -3.6885638E-12 1,midg,midg; igrid,midg,midg 2.2640832E-10 -1.4256032E-10 gauss-seidel spectral radius is 0.9797320 estimated iterations to convergence 58 setup time was (sec) 0.9300000 now iterating at: 22:57:08 rms-change max change #iterations 5.5608746E-02 9.966234 at 10iterations 3.1073573E-03 0.5587063 at 20iterations 2.6861555E-04 6.2006950E-02 at 30iterations 7.1617505E-05 1.9657612E-02 at 40iterations 2.3610153E-05 6.4744949E-03 at 50iterations finished qdiffx linear iterations at : 22:57:13 total time elapsed so far: 5.610000 # loops : 50 mean,max change (kT/e) : 2.3610153E-05 6.4744949E-03 energy calculations done at 5.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.830000 DelPhi exited at 22:57:14 5.831u 0.467s 0:06.81 92.3% 0+0k 0+0io 6pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 22:57:14 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4305 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.507559 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -21.94100 31.48900 ymin,ymax (A): -88.03900 -17.19600 zmin,zma (A): -64.11700 -0.2750000 x,y,z range (A): 53.43000 70.84300 63.84200 scale (grids/A): 1.507559 object centre (A): 4.774000 -52.61750 -32.19600 number of atom coordinates read : 4305 total number of charged atoms : 4145 net assigned charge : 2.000011 assigned positive charge : 648.7268 centred at (gu) : 88.51884 87.43517 95.36405 assigned negative charge : -646.7314 centred at (gu) : 88.84909 87.48223 95.52598 start vw surface at 0.2200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 79950 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41189 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 23199 mr = 53134 m= 1885 mr = 15087 m= 28 mr = 778 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8600000 number of dielectric boundary points 36063 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 572 ## 8 charges are in solution ## iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 30996 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5025197 object centre at (A) : 4.774000 -52.61750 -32.19600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8278665E-03 6.0739331E-03 midg,1,midg; midg,igrid,midg 9.9904984E-03 1.7449809E-02 1,midg,midg; igrid,midg,midg -7.8253588E-04 -8.5218512E-03 gauss-seidel spectral radius is 0.9980154 estimated iterations to convergence 178 setup time was (sec) 1.220000 now iterating at: 22:57:15 rms-change max change #iterations 3.400636 149.7542 at 10iterations 1.359876 53.43256 at 20iterations 0.5421450 22.34064 at 30iterations 0.2168178 7.985868 at 40iterations 8.6783163E-02 3.314649 at 50iterations 3.4777395E-02 1.196589 at 60iterations 1.3977600E-02 0.4654446 at 70iterations 5.6277695E-03 0.1978995 at 80iterations 2.2819166E-03 7.9860687E-02 at 90iterations 9.5027115E-04 3.4979820E-02 at 100iterations 4.1947706E-04 1.7131090E-02 at 110iterations 2.0826979E-04 1.0246277E-02 at 120iterations finished qdiffx linear iterations at : 22:57:26 total time elapsed so far: 12.16000 # loops : 120 mean,max change (kT/e) : 2.0826979E-04 1.0246277E-02 energy calculations done at 12.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.39000 DelPhi exited at 22:57:27 12.394u 0.506s 0:13.25 97.2% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 22:57:27 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4305 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.261338 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -21.94100 31.48900 ymin,ymax (A): -88.03900 -17.19600 zmin,zma (A): -64.11700 -0.2750000 x,y,z range (A): 53.43000 70.84300 63.84200 scale (grids/A): 2.261338 object centre (A): 4.774000 -52.61750 -32.19600 number of atom coordinates read : 4305 total number of charged atoms : 4145 net assigned charge : 2.000011 assigned positive charge : 648.7268 centred at (gu) : 87.77783 86.15226 98.04579 assigned negative charge : -646.7314 centred at (gu) : 88.27343 86.22331 98.28888 start vw surface at 0.2100000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 185994 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41189 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 83033 mr = 130962 m= 20714 mr = 63869 m= 2702 mr = 14730 m= 134 mr = 1597 m= 1 mr = 53 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.280000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.070000 number of dielectric boundary points 81368 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 2.240000 number of grid points assigned charge 33050 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.507559 object centre at (A) : 4.774000 -52.61750 -32.19600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1125558 0.1917424 midg,1,midg; midg,igrid,midg 0.3416114 0.4680813 1,midg,midg; igrid,midg,midg -2.0582605E-02 -0.1350856 gauss-seidel spectral radius is 0.9991261 estimated iterations to convergence 267 setup time was (sec) 2.470000 now iterating at: 22:57:30 rms-change max change #iterations 9.509117 307.1480 at 10iterations 5.447661 138.9627 at 20iterations 3.075578 73.40778 at 30iterations 1.725994 37.40282 at 40iterations 0.9613280 23.77154 at 50iterations 0.5367119 11.51321 at 60iterations 0.2967232 6.235424 at 70iterations 0.1639667 3.693776 at 80iterations 9.0738125E-02 1.949121 at 90iterations 4.9909130E-02 1.068710 at 100iterations 2.7463917E-02 0.5598850 at 110iterations 1.5101215E-02 0.3009977 at 120iterations 8.2997410E-03 0.1652136 at 130iterations 4.5909057E-03 0.1026459 at 140iterations 2.5366324E-03 4.8599958E-02 at 150iterations 1.4136094E-03 2.7679443E-02 at 160iterations 8.0223993E-04 1.8079758E-02 at 170iterations 4.6806157E-04 1.0099411E-02 at 180iterations finished qdiffx linear iterations at : 22:57:48 total time elapsed so far: 20.22000 # loops : 180 mean,max change (kT/e) : 4.6806157E-04 1.0099411E-02 energy calculations done at 20.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.44000 DelPhi exited at 22:57:49 20.447u 0.527s 0:22.11 94.7% 0+0k 0+0io 0pf+0w