Sun Oct 9 06:09:01 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 06:09:01 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1863 !!! WARNING: HIZ 148 has a net charge of 0.2000 !!! WARNING: HIZ 152 has a net charge of 0.2000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6759065 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): -8.484000 34.10500 ymin,ymax (A): 31.86300 84.53300 zmin,zma (A): -6.229000 40.31800 x,y,z range (A): 42.58900 52.67001 46.54700 scale (grids/A): 0.6759065 object centre (A): 12.81050 58.19800 17.04450 number of atom coordinates read : 1863 total number of charged atoms : 1731 net assigned charge : -6.099990 assigned positive charge : 278.9731 centred at (gu) : 90.47095 88.17046 89.67789 assigned negative charge : -285.0730 centred at (gu) : 90.51429 87.96908 89.58100 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5711 nv = 96 ne = 84 npr = 39012 no. pairs analyzed = 39012 no. exposed pairs = 2332 no. arc points = 16651 no. surface atoms = 792 nbur = 1071 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 315 mr = 3058 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.1600000 number of dielectric boundary points 2945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1518 ## 107 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6538 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6450712E-08 -1.7571248E-09 midg,1,midg; midg,igrid,midg -9.7347048E-08 1.3416619E-08 1,midg,midg; igrid,midg,midg -1.2049080E-08 -3.4963001E-08 gauss-seidel spectral radius is 0.9885849 estimated iterations to convergence 76 setup time was (sec) 0.3600000 now iterating at: 06:09:01 rms-change max change #iterations 0.1540674 24.70647 at 10iterations 1.7324401E-02 3.116793 at 20iterations 1.9655644E-03 0.3287849 at 30iterations 2.1103187E-04 3.2331467E-02 at 40iterations 2.3514816E-05 3.7841797E-03 at 50iterations finished qdiffx linear iterations at : 06:09:04 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 2.3514816E-05 3.7841797E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 06:09:05 3.533u 0.203s 0:04.01 93.0% 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 06:09:05 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1863 !!! WARNING: HIZ 148 has a net charge of 0.2000 !!! WARNING: HIZ 152 has a net charge of 0.2000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.027719 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): -8.484000 34.10500 ymin,ymax (A): 31.86300 84.53300 zmin,zma (A): -6.229000 40.31800 x,y,z range (A): 42.58900 52.67001 46.54700 scale (grids/A): 2.027719 object centre (A): 12.81050 58.19800 17.04450 number of atom coordinates read : 1863 total number of charged atoms : 1731 net assigned charge : -6.099990 assigned positive charge : 278.9731 centred at (gu) : 91.41290 84.51137 89.03374 assigned negative charge : -285.0730 centred at (gu) : 91.54295 83.90725 88.74294 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 61038 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16651 grid for indexing accessible points = 1.400000 m= 21055 mr = 41445 m= 3236 mr = 15040 m= 220 mr = 1924 m= 2 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 859 time to turn everything in is 0.3000000 number of dielectric boundary points 27051 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 61 iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 13707 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) : 0.6759065 object centre at (A) : 12.81050 58.19800 17.04450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6069635E-02 -1.8790308E-02 midg,1,midg; midg,igrid,midg -2.9889584E-02 8.0178849E-02 1,midg,midg; igrid,midg,midg -7.7188034E-03 -3.7086647E-02 gauss-seidel spectral radius is 0.9987129 estimated iterations to convergence 221 setup time was (sec) 0.5200000 now iterating at: 06:09:06 rms-change max change #iterations 4.018617 189.7469 at 10iterations 1.927695 71.88287 at 20iterations 0.9183835 35.27976 at 30iterations 0.4418726 15.57709 at 40iterations 0.2116519 8.414084 at 50iterations 0.1009148 3.933678 at 60iterations 4.8212174E-02 1.585785 at 70iterations 2.3115814E-02 0.7777691 at 80iterations 1.1061929E-02 0.3685894 at 90iterations 5.3137252E-03 0.1756964 at 100iterations 2.5376147E-03 8.4197283E-02 at 110iterations 1.2117837E-03 4.3952465E-02 at 120iterations finished qdiffx linear iterations at : 06:09:13 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 1.2117837E-03 4.3952465E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 06:09:14 7.685u 0.812s 0:08.77 96.8% 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 06:09:14 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1863 !!! WARNING: HIZ 148 has a net charge of 0.2000 !!! WARNING: HIZ 152 has a net charge of 0.2000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.041579 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): -8.484000 34.10500 ymin,ymax (A): 31.86300 84.53300 zmin,zma (A): -6.229000 40.31800 x,y,z range (A): 42.58900 52.67001 46.54700 scale (grids/A): 3.041579 object centre (A): 12.81050 58.19800 17.04450 number of atom coordinates read : 1863 total number of charged atoms : 1731 net assigned charge : -6.099990 assigned positive charge : 278.9731 centred at (gu) : 92.11943 81.76700 88.55058 assigned negative charge : -285.0730 centred at (gu) : 92.31441 80.86095 88.11436 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 141267 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16651 grid for indexing accessible points = 1.400000 m= 68788 mr = 100590 m= 23821 mr = 55503 m= 5732 mr = 18572 m= 888 mr = 4162 m= 93 mr = 610 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 3362 time to turn everything in is 0.8000000 number of dielectric boundary points 61100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 13848 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) : 2.027719 object centre at (A) : 12.81050 58.19800 17.04450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2483324 -6.2745146E-02 midg,1,midg; midg,igrid,midg -0.1369358 0.9112983 1,midg,midg; igrid,midg,midg -5.7496849E-02 -0.2900370 gauss-seidel spectral radius is 0.9992657 estimated iterations to convergence 291 setup time was (sec) 1.020000 now iterating at: 06:09:15 rms-change max change #iterations 9.120874 388.2913 at 10iterations 5.266229 148.8833 at 20iterations 3.039749 68.15060 at 30iterations 1.755496 35.03771 at 40iterations 1.012622 18.93906 at 50iterations 0.5807075 12.85564 at 60iterations 0.3351629 6.149699 at 70iterations 0.1928911 3.854425 at 80iterations 0.1106814 2.053144 at 90iterations 6.3709199E-02 1.269041 at 100iterations 3.6630251E-02 0.7111444 at 110iterations 2.1039644E-02 0.3938327 at 120iterations 1.2105514E-02 0.2648582 at 130iterations 6.9543663E-03 0.1472588 at 140iterations 3.9937366E-03 7.5603485E-02 at 150iterations 2.2944373E-03 4.5081735E-02 at 160iterations 1.3198529E-03 2.5425911E-02 at 170iterations 7.5954641E-04 1.4122009E-02 at 180iterations finished qdiffx linear iterations at : 06:09:27 total time elapsed so far: 12.20000 # loops : 180 mean,max change (kT/e) : 7.5954641E-04 1.4122009E-02 energy calculations done at 12.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.34000 DelPhi exited at 06:09:27 12.347u 0.980s 0:13.61 97.8% 0+0k 0+0io 0pf+0w