Mon Oct 10 17:00:31 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 17:00:31 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4297 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 825 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5089786 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): -16.88000 37.27200 ymin,ymax (A): -32.68300 30.40600 zmin,zma (A): -4.107000 65.83700 x,y,z range (A): 54.15200 63.08900 69.94400 scale (grids/A): 0.5089786 object centre (A): 10.19600 -1.138499 30.86500 number of atom coordinates read : 4297 total number of charged atoms : 4050 net assigned charge : 5.206038 assigned positive charge : 638.0684 centred at (gu) : 90.21900 91.10544 87.54967 assigned negative charge : -632.8661 centred at (gu) : 90.07635 91.12138 87.56953 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7113 nv = 96 ne = 84 npr = 86791 no. pairs analyzed = 86791 no. exposed pairs = 5630 no. arc points = 38888 no. surface atoms = 1884 nbur = 2413 mkacc time = 0.1800000 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 = 1.652000 m= 261 mr = 3623 m= 0 mr = 4 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3747 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3681 ## 545 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9389 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0835308E-10 1.3818950E-11 midg,1,midg; midg,igrid,midg 7.5540164E-11 4.3092009E-11 1,midg,midg; igrid,midg,midg -2.2807861E-10 3.8588036E-10 gauss-seidel spectral radius is 0.9802287 estimated iterations to convergence 59 setup time was (sec) 0.6100000 now iterating at: 17:00:32 rms-change max change #iterations 6.2306006E-02 10.34973 at 10iterations 3.5221563E-03 0.5602121 at 20iterations 3.6381037E-04 4.8133850E-02 at 30iterations 1.0761397E-04 1.2915075E-02 at 40iterations 3.8589089E-05 5.2700043E-03 at 50iterations finished qdiffx linear iterations at : 17:00:34 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 3.8589089E-05 5.2700043E-03 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 17:00:35 3.248u 0.167s 0:03.97 85.6% 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 17:00:35 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4297 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 825 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.526936 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): -16.88000 37.27200 ymin,ymax (A): -32.68300 30.40600 zmin,zma (A): -4.107000 65.83700 x,y,z range (A): 54.15200 63.08900 69.94400 scale (grids/A): 1.526936 object centre (A): 10.19600 -1.138499 30.86500 number of atom coordinates read : 4297 total number of charged atoms : 4050 net assigned charge : 5.206038 assigned positive charge : 638.0684 centred at (gu) : 90.65619 93.31523 82.64735 assigned negative charge : -632.8661 centred at (gu) : 90.22900 93.36407 82.70842 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 80627 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38888 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 22351 mr = 54805 m= 1816 mr = 14277 m= 44 mr = 708 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 35048 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 536 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 30447 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) : 0.5089786 object centre at (A) : 10.19600 -1.138499 30.86500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8962816E-03 9.6506951E-03 midg,1,midg; midg,igrid,midg -9.2261052E-04 -2.6456274E-03 1,midg,midg; igrid,midg,midg -3.2104468E-03 9.6556842E-03 gauss-seidel spectral radius is 0.9980561 estimated iterations to convergence 180 setup time was (sec) 0.8000000 now iterating at: 17:00:36 rms-change max change #iterations 3.470869 153.9449 at 10iterations 1.400241 53.52477 at 20iterations 0.5629843 20.08391 at 30iterations 0.2288902 7.925900 at 40iterations 9.2443787E-02 3.566757 at 50iterations 3.7488278E-02 1.310970 at 60iterations 1.5197974E-02 0.5065193 at 70iterations 6.1663319E-03 0.2590771 at 80iterations 2.5232986E-03 8.4837914E-02 at 90iterations 1.0457461E-03 3.4415007E-02 at 100iterations 4.4467882E-04 1.7097473E-02 at 110iterations 2.0396562E-04 7.4310303E-03 at 120iterations finished qdiffx linear iterations at : 17:00:42 total time elapsed so far: 6.960000 # loops : 120 mean,max change (kT/e) : 2.0396562E-04 7.4310303E-03 energy calculations done at 6.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.130000 DelPhi exited at 17:00:43 7.136u 0.189s 0:08.31 87.9% 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 17:00:44 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4297 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 825 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.290404 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): -16.88000 37.27200 ymin,ymax (A): -32.68300 30.40600 zmin,zma (A): -4.107000 65.83700 x,y,z range (A): 54.15200 63.08900 69.94400 scale (grids/A): 2.290404 object centre (A): 10.19600 -1.138499 30.86500 number of atom coordinates read : 4297 total number of charged atoms : 4050 net assigned charge : 5.206038 assigned positive charge : 638.0684 centred at (gu) : 90.98380 94.97255 78.97063 assigned negative charge : -632.8661 centred at (gu) : 90.34348 95.04613 79.06255 start vw surface at 0.2300000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 188145 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38888 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 81136 mr = 134884 m= 19213 mr = 62360 m= 2523 mr = 13379 m= 120 mr = 1438 m= 3 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.7500001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.340000 number of dielectric boundary points 79046 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 32306 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) : 1.526936 object centre at (A) : 10.19600 -1.138499 30.86500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2494595 0.2608465 midg,1,midg; midg,igrid,midg -9.7838387E-02 -0.1231990 1,midg,midg; igrid,midg,midg -4.6015065E-02 0.1293594 gauss-seidel spectral radius is 0.9991360 estimated iterations to convergence 269 setup time was (sec) 1.620000 now iterating at: 17:00:45 rms-change max change #iterations 9.557384 258.2901 at 10iterations 5.419107 144.0155 at 20iterations 3.058718 71.14957 at 30iterations 1.712940 38.27097 at 40iterations 0.9576442 22.15048 at 50iterations 0.5322143 12.08449 at 60iterations 0.2955916 6.314559 at 70iterations 0.1635010 3.594415 at 80iterations 9.0614960E-02 2.210562 at 90iterations 5.0051477E-02 1.099594 at 100iterations 2.7640957E-02 0.5679531 at 110iterations 1.5243405E-02 0.2984538 at 120iterations 8.4233750E-03 0.1648102 at 130iterations 4.6357005E-03 9.7760201E-02 at 140iterations 2.5506525E-03 5.1313400E-02 at 150iterations 1.4025338E-03 2.6586771E-02 at 160iterations 7.7439228E-04 1.5033722E-02 at 170iterations 4.2685831E-04 8.7256432E-03 at 180iterations finished qdiffx linear iterations at : 17:00:55 total time elapsed so far: 11.14000 # loops : 180 mean,max change (kT/e) : 4.2685831E-04 8.7256432E-03 energy calculations done at 11.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.32000 DelPhi exited at 17:00:55 11.324u 0.214s 0:11.94 96.5% 0+0k 0+0io 0pf+0w