Sun Oct 9 08:33:40 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 08:33:41 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 = 5540 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5264794 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): 3.370000 68.59100 ymin,ymax (A): 24.86900 89.57600 zmin,zma (A): 60.29300 127.9120 x,y,z range (A): 65.22100 64.70700 67.61899 scale (grids/A): 0.5264794 object centre (A): 35.98050 57.22250 94.10250 number of atom coordinates read : 5540 total number of charged atoms : 5374 net assigned charge : -5.499979 assigned positive charge : 831.2628 centred at (gu) : 89.29729 88.48895 89.62012 assigned negative charge : -836.7698 centred at (gu) : 89.37334 88.50240 89.48228 start vw surface at 0.2400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 9749 nv = 96 ne = 84 npr = 112353 no. pairs analyzed = 112353 no. exposed pairs = 6836 no. arc points = 47447 no. surface atoms = 2306 nbur = 3234 mkacc time = 0.3200000 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 = 1.624000 m= 402 mr = 5172 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.6300000 number of dielectric boundary points 4955 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4693 ## 641 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 13047 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0781299E-09 5.7654653E-10 midg,1,midg; midg,igrid,midg -1.1037664E-10 -1.6061476E-10 1,midg,midg; igrid,midg,midg 3.4425898E-10 -5.0544058E-10 gauss-seidel spectral radius is 0.9816008 estimated iterations to convergence 61 setup time was (sec) 0.8900000 now iterating at: 08:33:42 rms-change max change #iterations 8.4715717E-02 12.06492 at 10iterations 5.6195832E-03 0.7741103 at 20iterations 5.7337474E-04 0.1215477 at 30iterations 1.4389907E-04 3.3836365E-02 at 40iterations 4.5158991E-05 1.0074615E-02 at 50iterations finished qdiffx linear iterations at : 08:33:45 total time elapsed so far: 4.190000 # loops : 50 mean,max change (kT/e) : 4.5158991E-05 1.0074615E-02 energy calculations done at 4.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 08:33:45 4.378u 0.283s 0:04.93 94.3% 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 08:33:45 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 = 5540 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.579438 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): 3.370000 68.59100 ymin,ymax (A): 24.86900 89.57600 zmin,zma (A): 60.29300 127.9120 x,y,z range (A): 65.22100 64.70700 67.61899 scale (grids/A): 1.579438 object centre (A): 35.98050 57.22250 94.10250 number of atom coordinates read : 5540 total number of charged atoms : 5374 net assigned charge : -5.499979 assigned positive charge : 831.2628 centred at (gu) : 87.89008 85.46504 88.85835 assigned negative charge : -836.7698 centred at (gu) : 88.12001 85.50705 88.44659 start vw surface at 0.2300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 109286 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47447 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 32906 mr = 75629 m= 3385 mr = 22260 m= 90 mr = 1649 m= 0 mr = 5 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 677 time to turn everything in is 0.9400000 number of dielectric boundary points 46124 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 627 ## 10 charges are in solution ## iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 40843 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) : 0.5264794 object centre at (A) : 35.98050 57.22250 94.10250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9103639E-02 1.0331989E-02 midg,1,midg; midg,igrid,midg -1.3119806E-02 -1.2084438E-02 1,midg,midg; igrid,midg,midg 6.4001153E-03 2.6006210E-03 gauss-seidel spectral radius is 0.9983069 estimated iterations to convergence 193 setup time was (sec) 1.270000 now iterating at: 08:33:47 rms-change max change #iterations 4.421675 166.5912 at 10iterations 1.896658 62.80035 at 20iterations 0.8162867 25.77008 at 30iterations 0.3504045 10.10636 at 40iterations 0.1508909 4.341864 at 50iterations 6.4831175E-02 2.195633 at 60iterations 2.7932558E-02 0.7989547 at 70iterations 1.2018328E-02 0.3281708 at 80iterations 5.2081496E-03 0.1485718 at 90iterations 2.2748071E-03 6.4172745E-02 at 100iterations 9.9785894E-04 2.8291702E-02 at 110iterations 4.4956626E-04 1.5300751E-02 at 120iterations finished qdiffx linear iterations at : 08:33:56 total time elapsed so far: 9.990000 # loops : 120 mean,max change (kT/e) : 4.4956626E-04 1.5300751E-02 energy calculations done at 9.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.18000 DelPhi exited at 08:33:56 10.184u 0.312s 0:10.76 97.4% 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 08:33:56 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 = 5540 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.369157 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): 3.370000 68.59100 ymin,ymax (A): 24.86900 89.57600 zmin,zma (A): 60.29300 127.9120 x,y,z range (A): 65.22100 64.70700 67.61899 scale (grids/A): 2.369157 object centre (A): 35.98050 57.22250 94.10250 number of atom coordinates read : 5540 total number of charged atoms : 5374 net assigned charge : -5.499979 assigned positive charge : 831.2628 centred at (gu) : 86.83496 83.19705 88.28713 assigned negative charge : -836.7698 centred at (gu) : 87.17986 83.26048 87.66975 start vw surface at 0.2400000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 254262 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47447 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 116137 mr = 185305 m= 31735 mr = 91121 m= 5215 mr = 23627 m= 346 mr = 3519 m= 6 mr = 143 m= 0 mr = 0 time to grow re-entrant surface = 1.470000 no. cavity mid-points inaccessible to solvent = 2166 time to turn everything in is 2.390000 number of dielectric boundary points 103986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 2.560000 number of grid points assigned charge 42919 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) : 1.579438 object centre at (A) : 35.98050 57.22250 94.10250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5225159 9.0618834E-02 midg,1,midg; midg,igrid,midg -0.3588829 -0.1693336 1,midg,midg; igrid,midg,midg 0.2781037 0.2159415 gauss-seidel spectral radius is 0.9992417 estimated iterations to convergence 287 setup time was (sec) 2.740000 now iterating at: 08:33:59 rms-change max change #iterations 11.74721 311.4565 at 10iterations 6.944746 160.1061 at 20iterations 4.086798 85.43377 at 30iterations 2.394240 41.84843 at 40iterations 1.392787 27.15955 at 50iterations 0.8097424 14.62666 at 60iterations 0.4687581 8.624157 at 70iterations 0.2708402 4.566189 at 80iterations 0.1564314 2.594507 at 90iterations 9.0131596E-02 1.485198 at 100iterations 5.1855467E-02 0.8652725 at 110iterations 2.9814014E-02 0.5094490 at 120iterations 1.7131818E-02 0.2910753 at 130iterations 9.8503781E-03 0.1812820 at 140iterations 5.6631207E-03 9.5493317E-02 at 150iterations 3.2531694E-03 5.6397438E-02 at 160iterations 1.8752384E-03 3.1375051E-02 at 170iterations 1.0786211E-03 1.9330978E-02 at 180iterations finished qdiffx linear iterations at : 08:34:14 total time elapsed so far: 17.59000 # loops : 180 mean,max change (kT/e) : 1.0786211E-03 1.9330978E-02 energy calculations done at 17.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.78000 DelPhi exited at 08:34:15 17.778u 0.312s 0:18.34 98.5% 0+0k 0+0io 0pf+0w