Tue Oct 11 08:33:12 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 08:33:12 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 = 2017 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7054394 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): 10.97400 53.18200 ymin,ymax (A): 6.592000 48.09800 zmin,zma (A): 21.32700 71.79200 x,y,z range (A): 42.20800 41.50600 50.46500 scale (grids/A): 0.7054394 object centre (A): 32.07800 27.34500 46.55950 number of atom coordinates read : 2017 total number of charged atoms : 1992 net assigned charge : 6.500009 assigned positive charge : 322.2599 centred at (gu) : 90.94915 90.80029 90.47227 assigned negative charge : -315.7602 centred at (gu) : 91.04684 90.91869 90.54895 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6984 nv = 96 ne = 84 npr = 38425 no. pairs analyzed = 38425 no. exposed pairs = 2511 no. arc points = 17422 no. surface atoms = 860 nbur = 1157 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 480 mr = 4026 m= 2 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3359 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1711 ## 156 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7984 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2024513E-08 1.7922591E-08 midg,1,midg; midg,igrid,midg 9.3688378E-08 -4.9727449E-09 1,midg,midg; igrid,midg,midg 8.3025775E-08 7.0048318E-09 gauss-seidel spectral radius is 0.9895219 estimated iterations to convergence 80 setup time was (sec) 0.5400000 now iterating at: 08:33:13 rms-change max change #iterations 0.2009047 33.69609 at 10iterations 2.4579912E-02 3.522545 at 20iterations 3.0797950E-03 0.3820534 at 30iterations 4.3031143E-04 5.7564199E-02 at 40iterations 8.4559593E-05 1.2353897E-02 at 50iterations finished qdiffx linear iterations at : 08:33:16 total time elapsed so far: 3.810000 # loops : 50 mean,max change (kT/e) : 8.4559593E-05 1.2353897E-02 energy calculations done at 3.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 08:33:17 3.991u 0.283s 0:04.91 86.9% 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 Tue Oct 11 2011 at 08:33:17 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 = 2017 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.116318 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): 10.97400 53.18200 ymin,ymax (A): 6.592000 48.09800 zmin,zma (A): 21.32700 71.79200 x,y,z range (A): 42.20800 41.50600 50.46500 scale (grids/A): 2.116318 object centre (A): 32.07800 27.34500 46.55950 number of atom coordinates read : 2017 total number of charged atoms : 1992 net assigned charge : 6.500009 assigned positive charge : 322.2599 centred at (gu) : 92.84735 92.40079 91.41665 assigned negative charge : -315.7602 centred at (gu) : 93.14074 92.75608 91.64689 start vw surface at 0.1400000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 73879 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17422 grid for indexing accessible points = 1.400000 m= 30835 mr = 52563 m= 6026 mr = 23490 m= 522 mr = 3995 m= 13 mr = 261 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 30966 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 15822 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) : 0.7054394 object centre at (A) : 32.07800 27.34500 46.55950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0738353E-02 2.4821691E-02 midg,1,midg; midg,igrid,midg 2.5233734E-02 8.1460755E-03 1,midg,midg; igrid,midg,midg 4.0690180E-02 7.3581971E-03 gauss-seidel spectral radius is 0.9988226 estimated iterations to convergence 231 setup time was (sec) 0.9800000 now iterating at: 08:33:18 rms-change max change #iterations 4.613764 199.0419 at 10iterations 2.280462 71.90490 at 20iterations 1.127911 33.02103 at 30iterations 0.5603314 17.06165 at 40iterations 0.2776228 8.496154 at 50iterations 0.1375036 4.103191 at 60iterations 6.7956336E-02 2.487272 at 70iterations 3.3604011E-02 0.9869325 at 80iterations 1.6655130E-02 0.5044565 at 90iterations 8.2571898E-03 0.2503994 at 100iterations 4.1030971E-03 0.1248550 at 110iterations 2.0600185E-03 5.7870388E-02 at 120iterations finished qdiffx linear iterations at : 08:33:26 total time elapsed so far: 9.290000 # loops : 120 mean,max change (kT/e) : 2.0600185E-03 5.7870388E-02 energy calculations done at 9.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.460000 DelPhi exited at 08:33:27 9.466u 0.289s 0:10.14 96.0% 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 08:33:27 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 = 2017 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.174477 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): 10.97400 53.18200 ymin,ymax (A): 6.592000 48.09800 zmin,zma (A): 21.32700 71.79200 x,y,z range (A): 42.20800 41.50600 50.46500 scale (grids/A): 3.174477 object centre (A): 32.07800 27.34500 46.55950 number of atom coordinates read : 2017 total number of charged atoms : 1992 net assigned charge : 6.500009 assigned positive charge : 322.2599 centred at (gu) : 94.27101 93.60119 92.12489 assigned negative charge : -315.7602 centred at (gu) : 94.71109 94.13432 92.47037 start vw surface at 0.1400000 fill in re-entrant regions at 0.9300000 boundary points on vw surface= 170154 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17422 grid for indexing accessible points = 1.400000 m= 94579 mr = 126112 m= 39223 mr = 78938 m= 11405 mr = 32424 m= 2122 mr = 8740 m= 256 mr = 1554 m= 2 mr = 155 m= 0 mr = 0 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.170000 number of dielectric boundary points 69818 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.320000 number of grid points assigned charge 15936 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) : 2.116318 object centre at (A) : 32.07800 27.34500 46.55950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6247947 0.2033872 midg,1,midg; midg,igrid,midg 0.1818606 0.1274395 1,midg,midg; igrid,midg,midg 0.4020884 6.2398728E-02 gauss-seidel spectral radius is 0.9992967 estimated iterations to convergence 297 setup time was (sec) 2.490000 now iterating at: 08:33:30 rms-change max change #iterations 10.29554 363.0118 at 10iterations 6.090515 149.9366 at 20iterations 3.590309 81.85578 at 30iterations 2.118429 43.19064 at 40iterations 1.241490 22.54032 at 50iterations 0.7285423 14.05771 at 60iterations 0.4282365 7.223320 at 70iterations 0.2505264 4.543541 at 80iterations 0.1465224 2.605713 at 90iterations 8.5772961E-02 1.598160 at 100iterations 5.0294220E-02 0.9036136 at 110iterations 2.9417071E-02 0.6108932 at 120iterations 1.7285477E-02 0.3077316 at 130iterations 1.0172051E-02 0.1885090 at 140iterations 6.0528866E-03 0.1125646 at 150iterations 3.6483691E-03 6.4819336E-02 at 160iterations 2.2590023E-03 4.0597916E-02 at 170iterations 1.4530838E-03 2.7931213E-02 at 180iterations finished qdiffx linear iterations at : 08:33:43 total time elapsed so far: 16.18000 # loops : 180 mean,max change (kT/e) : 1.4530838E-03 2.7931213E-02 energy calculations done at 16.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.35000 DelPhi exited at 08:33:44 16.355u 0.311s 0:17.17 97.0% 0+0k 0+0io 0pf+0w