Sat Oct 8 11:35:15 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 Sat Oct 8 2011 at 11:35:15 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4471 !!! WARNING: HIQ 440 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5856901 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): -25.52200 35.04900 ymin,ymax (A): 35.00600 95.78900 zmin,zma (A): 31.14200 90.03100 x,y,z range (A): 60.57100 60.78300 58.88900 scale (grids/A): 0.5856901 object centre (A): 4.763500 65.39750 60.58650 number of atom coordinates read : 4471 total number of charged atoms : 4312 net assigned charge : -0.9859527 assigned positive charge : 673.9771 centred at (gu) : 90.83469 89.21872 88.45422 assigned negative charge : -674.9662 centred at (gu) : 90.69819 89.36697 88.62077 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 9764 nv = 96 ne = 84 npr = 94619 no. pairs analyzed = 94619 no. exposed pairs = 5054 no. arc points = 33874 no. surface atoms = 1726 nbur = 2745 mkacc time = 0.1600000 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 = 1.484000 m= 454 mr = 5699 m= 3 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.3100000 number of dielectric boundary points 4477 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3588 ## 363 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 12832 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8197716E-09 -5.0796252E-09 midg,1,midg; midg,igrid,midg 6.4879964E-09 -5.4342504E-09 1,midg,midg; igrid,midg,midg -4.9656825E-09 6.0149135E-09 gauss-seidel spectral radius is 0.9850571 estimated iterations to convergence 67 setup time was (sec) 0.5100000 now iterating at: 11:35:16 rms-change max change #iterations 0.1336348 17.60460 at 10iterations 1.0927171E-02 1.468176 at 20iterations 1.1134022E-03 0.1520538 at 30iterations 2.4635869E-04 3.0529976E-02 at 40iterations 8.7207205E-05 1.1366844E-02 at 50iterations finished qdiffx linear iterations at : 11:35:19 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 8.7207205E-05 1.1366844E-02 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 11:35:19 3.669u 0.196s 0:04.25 90.5% 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 Sat Oct 8 2011 at 11:35:19 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4471 !!! WARNING: HIQ 440 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.757070 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): -25.52200 35.04900 ymin,ymax (A): 35.00600 95.78900 zmin,zma (A): 31.14200 90.03100 x,y,z range (A): 60.57100 60.78300 58.88900 scale (grids/A): 1.757070 object centre (A): 4.763500 65.39750 60.58650 number of atom coordinates read : 4471 total number of charged atoms : 4312 net assigned charge : -0.9859527 assigned positive charge : 673.9771 centred at (gu) : 92.50289 87.65517 85.36099 assigned negative charge : -674.9662 centred at (gu) : 92.09420 88.10011 85.86144 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 108564 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33874 grid for indexing accessible points = 1.400000 m= 38084 mr = 78981 m= 5203 mr = 28246 m= 217 mr = 3184 m= 5 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 3375 time to turn everything in is 0.5100000 number of dielectric boundary points 41601 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 319 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 33583 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) : 0.5856901 object centre at (A) : 4.763500 65.39750 60.58650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1729649E-02 -3.5538301E-02 midg,1,midg; midg,igrid,midg 2.9976685E-02 -2.0692896E-02 1,midg,midg; igrid,midg,midg -8.7913191E-03 3.4602657E-02 gauss-seidel spectral radius is 0.9985628 estimated iterations to convergence 209 setup time was (sec) 0.7400000 now iterating at: 11:35:20 rms-change max change #iterations 4.967957 169.7289 at 10iterations 2.277892 75.62761 at 20iterations 1.047582 29.11388 at 30iterations 0.4818519 13.05982 at 40iterations 0.2219190 6.276058 at 50iterations 0.1021309 2.885101 at 60iterations 4.7147103E-02 1.268382 at 70iterations 2.1747438E-02 0.5744247 at 80iterations 1.0052213E-02 0.2709422 at 90iterations 4.6892478E-03 0.1305351 at 100iterations 2.2173014E-03 6.1172485E-02 at 110iterations 1.0752055E-03 2.9319286E-02 at 120iterations finished qdiffx linear iterations at : 11:35:28 total time elapsed so far: 8.210000 # loops : 120 mean,max change (kT/e) : 1.0752055E-03 2.9319286E-02 energy calculations done at 8.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.340000 DelPhi exited at 11:35:28 8.345u 0.221s 0:08.90 96.1% 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 Sat Oct 8 2011 at 11:35:28 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4471 !!! WARNING: HIQ 440 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.635605 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): -25.52200 35.04900 ymin,ymax (A): 35.00600 95.78900 zmin,zma (A): 31.14200 90.03100 x,y,z range (A): 60.57100 60.78300 58.88900 scale (grids/A): 2.635605 object centre (A): 4.763500 65.39750 60.58650 number of atom coordinates read : 4471 total number of charged atoms : 4312 net assigned charge : -0.9859527 assigned positive charge : 673.9771 centred at (gu) : 93.75378 86.48254 83.04144 assigned negative charge : -674.9662 centred at (gu) : 93.14114 87.15004 83.79211 start vw surface at 0.1200000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 251874 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33874 grid for indexing accessible points = 1.400000 m= 127215 mr = 191454 m= 42399 mr = 105086 m= 9155 mr = 33974 m= 1128 mr = 6915 m= 63 mr = 705 m= 0 mr = 19 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 11208 time to turn everything in is 1.330000 number of dielectric boundary points 93681 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 34485 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) : 1.757070 object centre at (A) : 4.763500 65.39750 60.58650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8999121 -0.4226357 midg,1,midg; midg,igrid,midg 0.3627446 -0.4554780 1,midg,midg; igrid,midg,midg -5.1455323E-02 0.2547268 gauss-seidel spectral radius is 0.9992694 estimated iterations to convergence 292 setup time was (sec) 1.590000 now iterating at: 11:35:30 rms-change max change #iterations 11.98456 295.4488 at 10iterations 7.071714 135.6689 at 20iterations 4.131392 74.87420 at 30iterations 2.408391 39.58416 at 40iterations 1.402050 25.09270 at 50iterations 0.8134082 13.46816 at 60iterations 0.4713506 7.568559 at 70iterations 0.2730705 4.760841 at 80iterations 0.1582526 2.698188 at 90iterations 9.1602631E-02 1.479160 at 100iterations 5.2964278E-02 0.8400269 at 110iterations 3.0649686E-02 0.4806561 at 120iterations 1.7726604E-02 0.2668724 at 130iterations 1.0261203E-02 0.1567001 at 140iterations 5.9683491E-03 9.5964432E-02 at 150iterations 3.4805585E-03 5.5236816E-02 at 160iterations 2.0513984E-03 3.2333374E-02 at 170iterations 1.2286732E-03 1.9045353E-02 at 180iterations finished qdiffx linear iterations at : 11:35:42 total time elapsed so far: 13.76000 # loops : 180 mean,max change (kT/e) : 1.2286732E-03 1.9045353E-02 energy calculations done at 13.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.88000 DelPhi exited at 11:35:43 13.885u 0.229s 0:14.58 96.7% 0+0k 0+0io 0pf+0w