Mon Oct 10 19:37:54 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+sph2.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 = amb2.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 Mon Oct 10 2011 at 19:37:54 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2797 !!! WARNING: SEP 83 has a net charge of -0.4750 !!! WARNING: HIR 243 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6209447 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): -27.03800 23.50400 ymin,ymax (A): -23.93100 28.20000 zmin,zma (A): 4.991000 62.32300 x,y,z range (A): 50.54200 52.13100 57.33200 scale (grids/A): 0.6209447 object centre (A): -1.767000 2.134501 33.65700 number of atom coordinates read : 2797 total number of charged atoms : 2658 net assigned charge : 3.9019674E-02 assigned positive charge : 413.1615 centred at (gu) : 87.35388 89.89819 88.59859 assigned negative charge : -413.1237 centred at (gu) : 87.43196 89.96771 88.53271 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7409 nv = 96 ne = 84 npr = 54215 no. pairs analyzed = 54215 no. exposed pairs = 4120 no. arc points = 29675 no. surface atoms = 1365 nbur = 1432 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 426 mr = 3502 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.2200000 number of dielectric boundary points 4297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2791 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8909 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6445032E-09 3.4036569E-09 midg,1,midg; midg,igrid,midg 5.0184119E-09 -4.9898432E-09 1,midg,midg; igrid,midg,midg 1.0069387E-08 -3.1951786E-09 gauss-seidel spectral radius is 0.9866062 estimated iterations to convergence 71 setup time was (sec) 0.4100000 now iterating at: 19:37:55 rms-change max change #iterations 0.1331128 22.54745 at 10iterations 1.2027293E-02 1.601940 at 20iterations 1.1233684E-03 0.1727142 at 30iterations 1.0822052E-04 1.6204834E-02 at 40iterations 1.1949047E-05 1.6660690E-03 at 50iterations finished qdiffx linear iterations at : 19:37:58 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.1949047E-05 1.6660690E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 19:37:58 3.435u 0.186s 0:03.95 91.3% 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 Mon Oct 10 2011 at 19:37:58 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2797 !!! WARNING: SEP 83 has a net charge of -0.4750 !!! WARNING: HIR 243 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.862834 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): -27.03800 23.50400 ymin,ymax (A): -23.93100 28.20000 zmin,zma (A): 4.991000 62.32300 x,y,z range (A): 50.54200 52.13100 57.33200 scale (grids/A): 1.862834 object centre (A): -1.767000 2.134501 33.65700 number of atom coordinates read : 2797 total number of charged atoms : 2658 net assigned charge : 3.9019674E-02 assigned positive charge : 413.1615 centred at (gu) : 82.06083 89.69405 85.79522 assigned negative charge : -413.1237 centred at (gu) : 82.29558 89.90303 85.59788 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79376 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29675 grid for indexing accessible points = 1.400000 m= 26693 mr = 50549 m= 4092 mr = 17764 m= 230 mr = 2222 m= 4 mr = 49 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 437 time to turn everything in is 0.4000000 number of dielectric boundary points 39812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20837 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) : 0.6209447 object centre at (A) : -1.767000 2.134501 33.65700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0593792E-02 2.2302086E-03 midg,1,midg; midg,igrid,midg 4.2167772E-03 -5.0452552E-03 1,midg,midg; igrid,midg,midg 2.5996291E-03 -1.0966869E-02 gauss-seidel spectral radius is 0.9986259 estimated iterations to convergence 214 setup time was (sec) 0.6100000 now iterating at: 19:37:59 rms-change max change #iterations 4.243915 169.3437 at 10iterations 1.968973 66.23543 at 20iterations 0.9138171 30.41590 at 30iterations 0.4249757 13.83256 at 40iterations 0.1978821 6.694672 at 50iterations 9.1752246E-02 2.935338 at 60iterations 4.2873785E-02 1.355640 at 70iterations 2.0009637E-02 0.6212883 at 80iterations 9.3446663E-03 0.2934091 at 90iterations 4.3480597E-03 0.1516075 at 100iterations 2.0279128E-03 7.3957205E-02 at 110iterations 9.4830623E-04 3.1014502E-02 at 120iterations finished qdiffx linear iterations at : 19:38:06 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 9.4830623E-04 3.1014502E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 19:38:07 7.969u 0.200s 0:08.70 93.7% 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 Mon Oct 10 2011 at 19:38:07 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2797 !!! WARNING: SEP 83 has a net charge of -0.4750 !!! WARNING: HIR 243 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.794251 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): -27.03800 23.50400 ymin,ymax (A): -23.93100 28.20000 zmin,zma (A): 4.991000 62.32300 x,y,z range (A): 50.54200 52.13100 57.33200 scale (grids/A): 2.794251 object centre (A): -1.767000 2.134501 33.65700 number of atom coordinates read : 2797 total number of charged atoms : 2658 net assigned charge : 3.9019674E-02 assigned positive charge : 413.1615 centred at (gu) : 78.09088 89.54081 83.69270 assigned negative charge : -413.1237 centred at (gu) : 78.44349 89.85444 83.39692 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 183529 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29675 grid for indexing accessible points = 1.400000 m= 85871 mr = 123867 m= 30298 mr = 65865 m= 7019 mr = 22633 m= 980 mr = 4748 m= 49 mr = 597 m= 0 mr = 9 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 1461 time to turn everything in is 0.9900000 number of dielectric boundary points 90027 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 21260 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) : 1.862834 object centre at (A) : -1.767000 2.134501 33.65700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5347452 2.5363471E-03 midg,1,midg; midg,igrid,midg 2.5355872E-02 -7.7934720E-02 1,midg,midg; igrid,midg,midg -0.2168586 -0.1827853 gauss-seidel spectral radius is 0.9992889 estimated iterations to convergence 296 setup time was (sec) 1.230000 now iterating at: 19:38:08 rms-change max change #iterations 10.34357 322.1320 at 10iterations 6.256433 139.5934 at 20iterations 3.733433 78.16562 at 30iterations 2.217753 44.15785 at 40iterations 1.312956 27.03067 at 50iterations 0.7725865 14.33815 at 60iterations 0.4552385 8.464046 at 70iterations 0.2661442 4.708330 at 80iterations 0.1559140 3.046484 at 90iterations 9.1161497E-02 1.934210 at 100iterations 5.3184737E-02 1.045137 at 110iterations 3.0979063E-02 0.5544710 at 120iterations 1.8018140E-02 0.3617635 at 130iterations 1.0509647E-02 0.2002907 at 140iterations 6.1175884E-03 0.1147728 at 150iterations 3.5607563E-03 6.4031124E-02 at 160iterations 2.0727590E-03 4.5745850E-02 at 170iterations 1.2095866E-03 2.1987915E-02 at 180iterations finished qdiffx linear iterations at : 19:38:20 total time elapsed so far: 12.98000 # loops : 180 mean,max change (kT/e) : 1.2095866E-03 2.1987915E-02 energy calculations done at 12.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.11000 DelPhi exited at 19:38:21 13.114u 0.225s 0:13.88 96.0% 0+0k 0+0io 0pf+0w