Sat Oct 8 22:53:20 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 Sat Oct 8 2011 at 22:53:20 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3266 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5740639 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): -15.88300 40.39700 ymin,ymax (A): 16.61100 76.28500 zmin,zma (A): 25.72000 87.73400 x,y,z range (A): 56.28000 59.67400 62.01400 scale (grids/A): 0.5740639 object centre (A): 12.25700 46.44800 56.72700 number of atom coordinates read : 3266 total number of charged atoms : 3126 net assigned charge : 14.95703 assigned positive charge : 480.4827 centred at (gu) : 89.86300 89.98222 90.61976 assigned negative charge : -465.5274 centred at (gu) : 89.73476 90.01178 90.85284 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7345 nv = 96 ne = 84 npr = 64318 no. pairs analyzed = 64318 no. exposed pairs = 4200 no. arc points = 30612 no. surface atoms = 1400 nbur = 1866 mkacc time = 0.2100000 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= 342 mr = 3807 m= 4 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.4700000 number of dielectric boundary points 3851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3076 ## 369 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 9289 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0322591E-09 -2.1555755E-09 midg,1,midg; midg,igrid,midg 3.2651850E-09 2.1261159E-09 1,midg,midg; igrid,midg,midg 2.3727892E-10 4.9211279E-09 gauss-seidel spectral radius is 0.9843755 estimated iterations to convergence 66 setup time was (sec) 0.8300000 now iterating at: 22:53:21 rms-change max change #iterations 9.8082215E-02 14.96336 at 10iterations 7.4211750E-03 1.156203 at 20iterations 5.8539788E-04 8.8497162E-02 at 30iterations 5.1848008E-05 7.2860718E-03 at 40iterations 6.1620658E-06 7.1406364E-04 at 50iterations finished qdiffx linear iterations at : 22:53:25 total time elapsed so far: 4.800000 # loops : 50 mean,max change (kT/e) : 6.1620658E-06 7.1406364E-04 energy calculations done at 4.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.040000 DelPhi exited at 22:53:26 5.046u 0.460s 0:05.83 94.3% 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 Sat Oct 8 2011 at 22:53:26 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3266 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.722192 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): -15.88300 40.39700 ymin,ymax (A): 16.61100 76.28500 zmin,zma (A): 25.72000 87.73400 x,y,z range (A): 56.28000 59.67400 62.01400 scale (grids/A): 1.722192 object centre (A): 12.25700 46.44800 56.72700 number of atom coordinates read : 3266 total number of charged atoms : 3126 net assigned charge : 14.95703 assigned positive charge : 480.4827 centred at (gu) : 89.58778 89.94580 91.85825 assigned negative charge : -465.5274 centred at (gu) : 89.20396 90.03516 92.55858 start vw surface at 0.2000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 80546 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30612 grid for indexing accessible points = 1.400000 m= 25659 mr = 54278 m= 3168 mr = 18008 m= 143 mr = 1780 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 2100 time to turn everything in is 0.8400000 number of dielectric boundary points 35421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 319 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 24250 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) : 0.5740639 object centre at (A) : 12.25700 46.44800 56.72700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1976714E-02 7.5522522E-03 midg,1,midg; midg,igrid,midg 4.0419076E-02 1.5210080E-02 1,midg,midg; igrid,midg,midg -7.2318334E-03 1.3830610E-02 gauss-seidel spectral radius is 0.9984193 estimated iterations to convergence 200 setup time was (sec) 1.190000 now iterating at: 22:53:27 rms-change max change #iterations 3.845411 163.6931 at 10iterations 1.689289 59.42374 at 20iterations 0.7453856 24.87481 at 30iterations 0.3282394 11.02767 at 40iterations 0.1445093 4.953846 at 50iterations 6.3876472E-02 2.013794 at 60iterations 2.8222555E-02 0.8755504 at 70iterations 1.2521126E-02 0.4073420 at 80iterations 5.5303494E-03 0.1870499 at 90iterations 2.4377555E-03 8.0001831E-02 at 100iterations 1.0817349E-03 3.1768799E-02 at 110iterations 4.7648707E-04 1.4391363E-02 at 120iterations finished qdiffx linear iterations at : 22:53:38 total time elapsed so far: 11.46000 # loops : 120 mean,max change (kT/e) : 4.7648707E-04 1.4391363E-02 energy calculations done at 11.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.67000 DelPhi exited at 22:53:38 11.676u 0.509s 0:12.49 97.4% 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 22:53:38 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3266 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.583288 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): -15.88300 40.39700 ymin,ymax (A): 16.61100 76.28500 zmin,zma (A): 25.72000 87.73400 x,y,z range (A): 56.28000 59.67400 62.01400 scale (grids/A): 2.583288 object centre (A): 12.25700 46.44800 56.72700 number of atom coordinates read : 3266 total number of charged atoms : 3126 net assigned charge : 14.95703 assigned positive charge : 480.4827 centred at (gu) : 89.38141 89.91861 92.78721 assigned negative charge : -465.5274 centred at (gu) : 88.80584 90.05264 93.83781 start vw surface at 0.1800000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 187192 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30612 grid for indexing accessible points = 1.400000 m= 87170 mr = 133309 m= 26889 mr = 69053 m= 5228 mr = 20710 m= 567 mr = 3672 m= 12 mr = 350 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 7157 time to turn everything in is 2.070000 number of dielectric boundary points 79964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 2.240000 number of grid points assigned charge 24985 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) : 1.722192 object centre at (A) : 12.25700 46.44800 56.72700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7109194 8.7813377E-02 midg,1,midg; midg,igrid,midg 0.6407623 0.2979372 1,midg,midg; igrid,midg,midg -6.2798530E-02 0.1945135 gauss-seidel spectral radius is 0.9992223 estimated iterations to convergence 283 setup time was (sec) 2.460000 now iterating at: 22:53:41 rms-change max change #iterations 9.655021 310.6556 at 10iterations 5.608579 143.1795 at 20iterations 3.235613 76.08734 at 30iterations 1.852983 40.95848 at 40iterations 1.061952 22.73430 at 50iterations 0.6056368 11.41526 at 60iterations 0.3453559 7.071022 at 70iterations 0.1967942 4.180705 at 80iterations 0.1119284 2.293228 at 90iterations 6.3625745E-02 1.198849 at 100iterations 3.6061805E-02 0.6630154 at 110iterations 2.0424770E-02 0.4375424 at 120iterations 1.1598982E-02 0.2175817 at 130iterations 6.5771989E-03 0.1186848 at 140iterations 3.7222689E-03 7.1055412E-02 at 150iterations 2.1080850E-03 3.8732529E-02 at 160iterations 1.1943689E-03 2.1976233E-02 at 170iterations 6.7622279E-04 1.4169693E-02 at 180iterations finished qdiffx linear iterations at : 22:53:59 total time elapsed so far: 20.63000 # loops : 180 mean,max change (kT/e) : 6.7622279E-04 1.4169693E-02 energy calculations done at 20.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.85000 DelPhi exited at 22:54:00 20.859u 0.553s 0:21.72 98.5% 0+0k 0+0io 0pf+0w