Mon Oct 10 14:19:24 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 14:19:25 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2399 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: 0.6223776 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): -7.881000 44.04600 ymin,ymax (A): 12.53100 69.73100 zmin,zma (A): 54.76600 106.6270 x,y,z range (A): 51.92700 57.20000 51.86100 scale (grids/A): 0.6223776 object centre (A): 18.08250 41.13100 80.69650 number of atom coordinates read : 2399 total number of charged atoms : 2240 net assigned charge : -3.999987 assigned positive charge : 350.8932 centred at (gu) : 90.01206 90.83640 90.05680 assigned negative charge : -354.8935 centred at (gu) : 89.77080 90.79050 90.03088 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6248 nv = 96 ne = 84 npr = 48886 no. pairs analyzed = 48886 no. exposed pairs = 3154 no. arc points = 22437 no. surface atoms = 1071 nbur = 1328 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 318 mr = 3209 m= 3 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3333 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2209 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7566 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.0996478E-09 -1.8082270E-09 midg,1,midg; midg,igrid,midg -5.4018634E-09 -5.5873817E-10 1,midg,midg; igrid,midg,midg -1.9558273E-08 1.1854199E-08 gauss-seidel spectral radius is 0.9866177 estimated iterations to convergence 71 setup time was (sec) 0.5900000 now iterating at: 14:19:26 rms-change max change #iterations 0.1209365 17.91253 at 10iterations 1.1154336E-02 1.732824 at 20iterations 1.0380781E-03 0.1804199 at 30iterations 9.5892021E-05 1.5066147E-02 at 40iterations 9.0475596E-06 1.4991760E-03 at 50iterations finished qdiffx linear iterations at : 14:19:29 total time elapsed so far: 4.430000 # loops : 50 mean,max change (kT/e) : 9.0475596E-06 1.4991760E-03 energy calculations done at 4.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.590000 DelPhi exited at 14:19:30 4.592u 0.406s 0:05.36 93.0% 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 Mon Oct 10 2011 at 14:19:30 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2399 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: 1.867133 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): -7.881000 44.04600 ymin,ymax (A): 12.53100 69.73100 zmin,zma (A): 54.76600 106.6270 x,y,z range (A): 51.92700 57.20000 51.86100 scale (grids/A): 1.867133 object centre (A): 18.08250 41.13100 80.69650 number of atom coordinates read : 2399 total number of charged atoms : 2240 net assigned charge : -3.999987 assigned positive charge : 350.8932 centred at (gu) : 90.03571 92.50893 90.17014 assigned negative charge : -354.8935 centred at (gu) : 89.31221 92.37115 90.09234 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 67691 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22437 grid for indexing accessible points = 1.400000 m= 22427 mr = 45409 m= 3005 mr = 15613 m= 151 mr = 1446 m= 6 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 30771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 173 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 17599 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) : 0.6223776 object centre at (A) : 18.08250 41.13100 80.69650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6128976E-02 -3.2267327E-04 midg,1,midg; midg,igrid,midg 2.0228182E-03 -3.0750227E-03 1,midg,midg; igrid,midg,midg -3.7961185E-02 7.9212645E-03 gauss-seidel spectral radius is 0.9985650 estimated iterations to convergence 209 setup time was (sec) 0.9100000 now iterating at: 14:19:31 rms-change max change #iterations 3.857781 157.6994 at 10iterations 1.763494 61.48667 at 20iterations 0.8101358 26.48782 at 30iterations 0.3723864 13.20655 at 40iterations 0.1704700 6.146290 at 50iterations 7.8400843E-02 2.626891 at 60iterations 3.5939965E-02 1.161277 at 70iterations 1.6544856E-02 0.6180649 at 80iterations 7.5770351E-03 0.2560902 at 90iterations 3.4650627E-03 0.1168289 at 100iterations 1.6006306E-03 5.6586266E-02 at 110iterations 7.3449546E-04 2.3232460E-02 at 120iterations finished qdiffx linear iterations at : 14:19:41 total time elapsed so far: 10.95000 # loops : 120 mean,max change (kT/e) : 7.3449546E-04 2.3232460E-02 energy calculations done at 10.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.12000 DelPhi exited at 14:19:42 11.125u 0.432s 0:12.05 95.8% 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 Mon Oct 10 2011 at 14:19:42 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2399 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: 2.800699 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): -7.881000 44.04600 ymin,ymax (A): 12.53100 69.73100 zmin,zma (A): 54.76600 106.6270 x,y,z range (A): 51.92700 57.20000 51.86100 scale (grids/A): 2.800699 object centre (A): 18.08250 41.13100 80.69650 number of atom coordinates read : 2399 total number of charged atoms : 2240 net assigned charge : -3.999987 assigned positive charge : 350.8932 centred at (gu) : 90.05356 93.76327 90.25491 assigned negative charge : -354.8935 centred at (gu) : 88.96835 93.55661 90.13844 start vw surface at 0.1100000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 156797 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22437 grid for indexing accessible points = 1.400000 m= 74738 mr = 110996 m= 24217 mr = 59391 m= 4794 mr = 18156 m= 571 mr = 3012 m= 33 mr = 270 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.560000 number of dielectric boundary points 69314 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 17919 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) : 1.867133 object centre at (A) : 18.08250 41.13100 80.69650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2548054 -6.7136427E-03 midg,1,midg; midg,igrid,midg 0.1144390 -0.1015709 1,midg,midg; igrid,midg,midg -0.3913800 3.2621842E-02 gauss-seidel spectral radius is 0.9992434 estimated iterations to convergence 287 setup time was (sec) 2.180000 now iterating at: 14:19:45 rms-change max change #iterations 9.317484 477.4521 at 10iterations 5.457345 126.0399 at 20iterations 3.172202 71.74788 at 30iterations 1.830273 41.37093 at 40iterations 1.057105 24.02088 at 50iterations 0.6080831 13.06243 at 60iterations 0.3492391 6.998214 at 70iterations 0.2003366 4.293724 at 80iterations 0.1149296 2.290451 at 90iterations 6.5747201E-02 1.372910 at 100iterations 3.7593324E-02 0.8283484 at 110iterations 2.1479391E-02 0.4367723 at 120iterations 1.2300452E-02 0.2566071 at 130iterations 7.0083421E-03 0.1364174 at 140iterations 4.0087756E-03 8.1432343E-02 at 150iterations 2.2852093E-03 5.0359726E-02 at 160iterations 1.3064990E-03 3.1287909E-02 at 170iterations 7.4630149E-04 1.3804436E-02 at 180iterations finished qdiffx linear iterations at : 14:20:13 total time elapsed so far: 30.39000 # loops : 180 mean,max change (kT/e) : 7.4630149E-04 1.3804436E-02 energy calculations done at 30.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 30.55000 DelPhi exited at 14:20:14 30.556u 0.780s 0:32.06 97.7% 0+0k 0+0io 0pf+0w