Tue Oct 11 06:55:24 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 Tue Oct 11 2011 at 06:55:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5487053 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): -20.37200 44.50800 ymin,ymax (A): 21.77200 78.11800 zmin,zma (A): -71.06300 -24.01900 x,y,z range (A): 64.88000 56.34600 47.04400 scale (grids/A): 0.5487053 object centre (A): 12.06800 49.94500 -47.54100 number of atom coordinates read : 2943 total number of charged atoms : 2803 net assigned charge : -1.499993 assigned positive charge : 427.9687 centred at (gu) : 89.78525 89.97614 89.81146 assigned negative charge : -429.4692 centred at (gu) : 89.78349 90.06261 89.82714 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5798 nv = 96 ne = 84 npr = 60602 no. pairs analyzed = 60602 no. exposed pairs = 3641 no. arc points = 25654 no. surface atoms = 1232 nbur = 1711 mkacc time = 0.1400000 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 = 1.568000 m= 220 mr = 3057 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3600000 number of dielectric boundary points 2940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2562 ## 290 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7495 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.8225742E-12 -2.0602586E-10 midg,1,midg; midg,igrid,midg 5.0738586E-10 -7.2143519E-10 1,midg,midg; igrid,midg,midg -1.2275639E-10 -8.6963312E-11 gauss-seidel spectral radius is 0.9828740 estimated iterations to convergence 63 setup time was (sec) 0.5900000 now iterating at: 06:55:25 rms-change max change #iterations 7.2440483E-02 14.35337 at 10iterations 5.0622197E-03 0.7938910 at 20iterations 4.1644325E-04 8.7728500E-02 at 30iterations 6.3456813E-05 1.5645266E-02 at 40iterations 1.5176899E-05 3.9243698E-03 at 50iterations finished qdiffx linear iterations at : 06:55:28 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.5176899E-05 3.9243698E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 06:55:28 3.467u 0.183s 0:04.24 85.8% 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 Tue Oct 11 2011 at 06:55:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.646116 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): -20.37200 44.50800 ymin,ymax (A): 21.77200 78.11800 zmin,zma (A): -71.06300 -24.01900 x,y,z range (A): 64.88000 56.34600 47.04400 scale (grids/A): 1.646116 object centre (A): 12.06800 49.94500 -47.54100 number of atom coordinates read : 2943 total number of charged atoms : 2803 net assigned charge : -1.499993 assigned positive charge : 427.9687 centred at (gu) : 89.35522 89.92761 89.43380 assigned negative charge : -429.4692 centred at (gu) : 89.35006 90.18757 89.48126 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 63758 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25654 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20725 mr = 43415 m= 2324 mr = 14755 m= 51 mr = 1253 m= 0 mr = 4 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 27431 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 239 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 21549 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) : 0.5487053 object centre at (A) : 12.06800 49.94500 -47.54100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2375437E-03 8.4431218E-03 midg,1,midg; midg,igrid,midg -3.5166170E-03 2.7984192E-03 1,midg,midg; igrid,midg,midg -2.1512948E-03 -2.1931138E-02 gauss-seidel spectral radius is 0.9982156 estimated iterations to convergence 188 setup time was (sec) 0.7800000 now iterating at: 06:55:29 rms-change max change #iterations 3.311066 141.3398 at 10iterations 1.389423 53.34988 at 20iterations 0.5815146 21.59320 at 30iterations 0.2449772 9.763996 at 40iterations 0.1031613 3.634760 at 50iterations 4.3481518E-02 1.554718 at 60iterations 1.8262491E-02 0.7035675 at 70iterations 7.6967427E-03 0.2896781 at 80iterations 3.2495470E-03 0.1116457 at 90iterations 1.3690342E-03 5.3273201E-02 at 100iterations 5.8080046E-04 2.3403168E-02 at 110iterations 2.4912681E-04 8.8028908E-03 at 120iterations finished qdiffx linear iterations at : 06:55:36 total time elapsed so far: 7.250000 # loops : 120 mean,max change (kT/e) : 2.4912681E-04 8.8028908E-03 energy calculations done at 7.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 06:55:36 7.460u 0.156s 0:07.90 96.3% 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 Tue Oct 11 2011 at 06:55:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.469174 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): -20.37200 44.50800 ymin,ymax (A): 21.77200 78.11800 zmin,zma (A): -71.06300 -24.01900 x,y,z range (A): 64.88000 56.34600 47.04400 scale (grids/A): 2.469174 object centre (A): 12.06800 49.94500 -47.54100 number of atom coordinates read : 2943 total number of charged atoms : 2803 net assigned charge : -1.499993 assigned positive charge : 427.9687 centred at (gu) : 89.03280 89.89139 89.15060 assigned negative charge : -429.4692 centred at (gu) : 89.02481 90.28117 89.22190 start vw surface at 0.1700000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 147920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25654 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 70260 mr = 105811 m= 21249 mr = 56480 m= 3677 mr = 16576 m= 214 mr = 2536 m= 2 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.150000 number of dielectric boundary points 61832 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 22388 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) : 1.646116 object centre at (A) : 12.06800 49.94500 -47.54100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1042994 0.1410047 midg,1,midg; midg,igrid,midg -4.5672130E-02 3.6329780E-02 1,midg,midg; igrid,midg,midg -5.3213466E-02 -0.3848948 gauss-seidel spectral radius is 0.9991479 estimated iterations to convergence 271 setup time was (sec) 1.440000 now iterating at: 06:55:38 rms-change max change #iterations 8.512396 277.6112 at 10iterations 4.753633 129.5812 at 20iterations 2.645354 67.23764 at 30iterations 1.468150 32.63062 at 40iterations 0.8130727 17.74353 at 50iterations 0.4503824 10.10846 at 60iterations 0.2488156 5.429001 at 70iterations 0.1370401 2.763702 at 80iterations 7.5828969E-02 1.476172 at 90iterations 4.1758746E-02 0.8640184 at 100iterations 2.3043394E-02 0.4861207 at 110iterations 1.2696684E-02 0.2589502 at 120iterations 6.9865282E-03 0.1625650 at 130iterations 3.8492377E-03 8.4396362E-02 at 140iterations 2.1237489E-03 4.4792175E-02 at 150iterations 1.1683496E-03 2.5419474E-02 at 160iterations 6.4489542E-04 1.3672352E-02 at 170iterations 3.5463029E-04 7.3022842E-03 at 180iterations finished qdiffx linear iterations at : 06:55:48 total time elapsed so far: 11.36000 # loops : 180 mean,max change (kT/e) : 3.5463029E-04 7.3022842E-03 energy calculations done at 11.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.55000 DelPhi exited at 06:55:49 11.552u 0.178s 0:12.22 95.9% 0+0k 0+0io 0pf+0w