Mon Oct 10 22:16:26 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 Mon Oct 10 2011 at 22:16:26 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: 238 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2766 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5393449 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): 14.77200 80.77800 ymin,ymax (A): -9.947000 43.33300 zmin,zma (A): -8.021000 35.07700 x,y,z range (A): 66.00600 53.28000 43.09800 scale (grids/A): 0.5393449 object centre (A): 47.77500 16.69300 13.52800 number of atom coordinates read : 2766 total number of charged atoms : 2620 net assigned charge : 7.500030 assigned positive charge : 418.8275 centred at (gu) : 88.13840 89.72653 90.17064 assigned negative charge : -411.3282 centred at (gu) : 88.35044 89.85452 90.33226 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5108 nv = 96 ne = 84 npr = 55714 no. pairs analyzed = 55714 no. exposed pairs = 3288 no. arc points = 23107 no. surface atoms = 1113 nbur = 1653 mkacc time = 0.1700000 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 = 1.596000 m= 194 mr = 2739 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 2548 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2296 ## 327 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 6692 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0477207E-09 -4.6912840E-10 midg,1,midg; midg,igrid,midg 1.0054321E-09 -2.6197086E-10 1,midg,midg; igrid,midg,midg 2.1229305E-09 -4.3314671E-10 gauss-seidel spectral radius is 0.9822593 estimated iterations to convergence 62 setup time was (sec) 0.6500000 now iterating at: 22:16:27 rms-change max change #iterations 6.7477509E-02 11.64867 at 10iterations 4.9125939E-03 0.8494568 at 20iterations 5.5151776E-04 0.1443291 at 30iterations 9.4011964E-05 2.7744293E-02 at 40iterations 1.7710712E-05 5.3100586E-03 at 50iterations finished qdiffx linear iterations at : 22:16:30 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 1.7710712E-05 5.3100586E-03 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 22:16:30 4.061u 0.166s 0:04.62 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 22:16:30 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: 238 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2766 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.618035 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): 14.77200 80.77800 ymin,ymax (A): -9.947000 43.33300 zmin,zma (A): -8.021000 35.07700 x,y,z range (A): 66.00600 53.28000 43.09800 scale (grids/A): 1.618035 object centre (A): 47.77500 16.69300 13.52800 number of atom coordinates read : 2766 total number of charged atoms : 2620 net assigned charge : 7.500030 assigned positive charge : 418.8275 centred at (gu) : 84.41465 89.17915 90.51131 assigned negative charge : -411.3282 centred at (gu) : 85.05077 89.56305 90.99668 start vw surface at 0.2200000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 57983 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23107 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 16922 mr = 40360 m= 1539 mr = 11828 m= 36 mr = 778 m= 0 mr = 2 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 834 time to turn everything in is 0.5800000 number of dielectric boundary points 23512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 256 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 19959 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) : 0.5393449 object centre at (A) : 47.77500 16.69300 13.52800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1041204E-02 4.5086650E-04 midg,1,midg; midg,igrid,midg 1.2556633E-02 -4.8350245E-03 1,midg,midg; igrid,midg,midg 5.8759549E-03 -5.8837730E-04 gauss-seidel spectral radius is 0.9981181 estimated iterations to convergence 183 setup time was (sec) 0.9300000 now iterating at: 22:16:31 rms-change max change #iterations 3.141779 170.5944 at 10iterations 1.290606 53.18372 at 20iterations 0.5272426 19.96650 at 30iterations 0.2165487 8.056637 at 40iterations 8.9575008E-02 3.496002 at 50iterations 3.6871240E-02 1.395879 at 60iterations 1.5293868E-02 0.5650939 at 70iterations 6.3885385E-03 0.2427254 at 80iterations 2.7134593E-03 0.1100731 at 90iterations 1.2119181E-03 5.3409576E-02 at 100iterations 5.7127990E-04 2.5947571E-02 at 110iterations 2.8396791E-04 1.5277863E-02 at 120iterations finished qdiffx linear iterations at : 22:16:40 total time elapsed so far: 9.040000 # loops : 120 mean,max change (kT/e) : 2.8396791E-04 1.5277863E-02 energy calculations done at 9.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.270000 DelPhi exited at 22:16:40 9.277u 0.230s 0:09.92 95.7% 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 22:16:40 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: 238 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2766 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.427052 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): 14.77200 80.77800 ymin,ymax (A): -9.947000 43.33300 zmin,zma (A): -8.021000 35.07700 x,y,z range (A): 66.00600 53.28000 43.09800 scale (grids/A): 2.427052 object centre (A): 47.77500 16.69300 13.52800 number of atom coordinates read : 2766 total number of charged atoms : 2620 net assigned charge : 7.500030 assigned positive charge : 418.8275 centred at (gu) : 81.62196 88.76839 90.76685 assigned negative charge : -411.3282 centred at (gu) : 82.57616 89.34451 91.49476 start vw surface at 0.2100000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 134593 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23107 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 60622 mr = 98069 m= 16047 mr = 48813 m= 2430 mr = 12090 m= 145 mr = 1640 m= 5 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 3030 time to turn everything in is 1.290000 number of dielectric boundary points 53180 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 20927 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) : 1.618035 object centre at (A) : 47.77500 16.69300 13.52800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1516950 6.2019113E-03 midg,1,midg; midg,igrid,midg 0.1558273 -0.1214931 1,midg,midg; igrid,midg,midg -1.5769759E-02 4.6619359E-02 gauss-seidel spectral radius is 0.9991023 estimated iterations to convergence 264 setup time was (sec) 1.660000 now iterating at: 22:16:42 rms-change max change #iterations 7.962219 241.6664 at 10iterations 4.367609 102.7387 at 20iterations 2.385751 54.34717 at 30iterations 1.296548 28.83819 at 40iterations 0.7061162 15.04603 at 50iterations 0.3838695 9.054275 at 60iterations 0.2090940 4.934687 at 70iterations 0.1135941 2.467670 at 80iterations 6.1617658E-02 1.460621 at 90iterations 3.3478223E-02 0.7554436 at 100iterations 1.8235905E-02 0.4173584 at 110iterations 9.9405004E-03 0.2376099 at 120iterations 5.4460787E-03 0.1414108 at 130iterations 3.0056783E-03 6.8679810E-02 at 140iterations 1.6867884E-03 4.8545837E-02 at 150iterations 9.6738397E-04 2.7072906E-02 at 160iterations 5.7277398E-04 1.5818119E-02 at 170iterations 3.5315743E-04 1.0936737E-02 at 180iterations finished qdiffx linear iterations at : 22:16:55 total time elapsed so far: 14.71000 # loops : 180 mean,max change (kT/e) : 3.5315743E-04 1.0936737E-02 energy calculations done at 14.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.95000 DelPhi exited at 22:16:57 14.956u 0.306s 0:16.36 93.2% 0+0k 0+0io 0pf+0w