Sat Oct 8 17:48:29 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 17:48:29 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3440 !!! WARNING: SEP 320 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5123776 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): -5.706000 63.77400 ymin,ymax (A): 16.11800 72.17500 zmin,zma (A): -13.31200 34.38300 x,y,z range (A): 69.48000 56.05700 47.69500 scale (grids/A): 0.5123776 object centre (A): 29.03400 44.14650 10.53550 number of atom coordinates read : 3440 total number of charged atoms : 3293 net assigned charge : -7.474987 assigned positive charge : 520.1472 centred at (gu) : 90.41873 87.61935 89.44268 assigned negative charge : -527.6238 centred at (gu) : 90.39162 87.63171 89.44875 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5707 nv = 96 ne = 84 npr = 70410 no. pairs analyzed = 70410 no. exposed pairs = 4201 no. arc points = 28988 no. surface atoms = 1426 nbur = 2014 mkacc time = 0.1200000 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= 212 mr = 3008 m= 0 mr = 3 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2908 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2888 ## 445 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 7629 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1812845E-10 -1.1050986E-10 midg,1,midg; midg,igrid,midg -1.6466899E-10 -7.6710020E-11 1,midg,midg; igrid,midg,midg -1.5325489E-10 -6.5966413E-11 gauss-seidel spectral radius is 0.9804190 estimated iterations to convergence 59 setup time was (sec) 0.4300000 now iterating at: 17:48:29 rms-change max change #iterations 5.9024841E-02 11.31872 at 10iterations 3.3398152E-03 0.8041387 at 20iterations 2.1935307E-04 3.9941788E-02 at 30iterations 3.2436903E-05 7.6763630E-03 at 40iterations 7.6574725E-06 1.9202232E-03 at 50iterations finished qdiffx linear iterations at : 17:48:32 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 7.6574725E-06 1.9202232E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 17:48:32 3.446u 0.174s 0:03.91 92.3% 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 Sat Oct 8 2011 at 17:48:33 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3440 !!! WARNING: SEP 320 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.537133 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): -5.706000 63.77400 ymin,ymax (A): 16.11800 72.17500 zmin,zma (A): -13.31200 34.38300 x,y,z range (A): 69.48000 56.05700 47.69500 scale (grids/A): 1.537133 object centre (A): 29.03400 44.14650 10.53550 number of atom coordinates read : 3440 total number of charged atoms : 3293 net assigned charge : -7.474987 assigned positive charge : 520.1472 centred at (gu) : 91.25513 82.85722 88.32719 assigned negative charge : -527.6238 centred at (gu) : 91.17430 82.89503 88.34597 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 64264 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28988 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 19021 mr = 44298 m= 1748 mr = 12931 m= 30 mr = 728 m= 0 mr = 3 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 301 time to turn everything in is 0.3200000 number of dielectric boundary points 27103 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 411 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 24728 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) : 0.5123776 object centre at (A) : 29.03400 44.14650 10.53550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0989630E-03 -6.0958002E-04 midg,1,midg; midg,igrid,midg -1.2649475E-02 -1.1780629E-02 1,midg,midg; igrid,midg,midg 7.4102939E-03 -4.7589927E-03 gauss-seidel spectral radius is 0.9979768 estimated iterations to convergence 177 setup time was (sec) 0.5300000 now iterating at: 17:48:33 rms-change max change #iterations 3.193722 194.8610 at 10iterations 1.264111 50.35887 at 20iterations 0.5047901 18.73648 at 30iterations 0.2011235 7.308226 at 40iterations 8.0085024E-02 2.865040 at 50iterations 3.1907428E-02 1.246769 at 60iterations 1.2649572E-02 0.4556618 at 70iterations 5.0770920E-03 0.2073288 at 80iterations 2.0177038E-03 7.1109772E-02 at 90iterations 8.1112125E-04 2.9257298E-02 at 100iterations 3.2770817E-04 1.3107777E-02 at 110iterations 1.3550049E-04 5.8593750E-03 at 120iterations finished qdiffx linear iterations at : 17:48:40 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 1.3550049E-04 5.8593750E-03 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 17:48:41 7.647u 0.210s 0:08.19 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 Sat Oct 8 2011 at 17:48:41 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3440 !!! WARNING: SEP 320 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.305699 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): -5.706000 63.77400 ymin,ymax (A): 16.11800 72.17500 zmin,zma (A): -13.31200 34.38300 x,y,z range (A): 69.48000 56.05700 47.69500 scale (grids/A): 2.305699 object centre (A): 29.03400 44.14650 10.53550 number of atom coordinates read : 3440 total number of charged atoms : 3293 net assigned charge : -7.474987 assigned positive charge : 520.1472 centred at (gu) : 91.88254 79.28551 87.49052 assigned negative charge : -527.6238 centred at (gu) : 91.76144 79.34224 87.51889 start vw surface at 0.1000000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 149772 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28988 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 67813 mr = 108858 m= 17448 mr = 53388 m= 2467 mr = 12715 m= 144 mr = 1514 m= 3 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 1078 time to turn everything in is 0.7700000 number of dielectric boundary points 61126 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 26273 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) : 1.537133 object centre at (A) : 29.03400 44.14650 10.53550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4216784E-03 2.9399439E-03 midg,1,midg; midg,igrid,midg -0.2405816 -0.2563491 1,midg,midg; igrid,midg,midg 0.5058697 -9.6748032E-02 gauss-seidel spectral radius is 0.9990748 estimated iterations to convergence 260 setup time was (sec) 1.000000 now iterating at: 17:48:42 rms-change max change #iterations 8.521560 268.7036 at 10iterations 4.692935 125.1993 at 20iterations 2.567920 75.30164 at 30iterations 1.395083 34.51217 at 40iterations 0.7563519 18.49295 at 50iterations 0.4098796 8.999574 at 60iterations 0.2216893 5.581468 at 70iterations 0.1197266 2.631279 at 80iterations 6.4465828E-02 1.377505 at 90iterations 3.4788698E-02 0.7328014 at 100iterations 1.8722311E-02 0.3791690 at 110iterations 1.0077612E-02 0.2009931 at 120iterations 5.4175840E-03 0.1262321 at 130iterations 2.9224937E-03 5.9988499E-02 at 140iterations 1.5719360E-03 3.3157349E-02 at 150iterations 8.4728276E-04 1.7227650E-02 at 160iterations 4.5521112E-04 1.0081768E-02 at 170iterations 2.4598668E-04 5.6467056E-03 at 180iterations finished qdiffx linear iterations at : 17:48:53 total time elapsed so far: 12.02000 # loops : 180 mean,max change (kT/e) : 2.4598668E-04 5.6467056E-03 energy calculations done at 12.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.15000 DelPhi exited at 17:48:53 12.157u 0.205s 0:12.67 97.4% 0+0k 0+0io 0pf+0w