Sun Oct 9 03:10:27 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 Sun Oct 9 2011 at 03:10:27 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4604 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: 0.5200725 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): 215.0780 276.0170 ymin,ymax (A): 71.70100 140.1530 zmin,zma (A): -70.09200 -6.305000 x,y,z range (A): 60.93901 68.45200 63.78700 scale (grids/A): 0.5200725 object centre (A): 245.5475 105.9270 -38.19850 number of atom coordinates read : 4604 total number of charged atoms : 4429 net assigned charge : 18.49995 assigned positive charge : 682.1505 centred at (gu) : 91.28925 87.40146 90.89742 assigned negative charge : -663.6559 centred at (gu) : 91.36717 87.39980 90.97933 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7801 nv = 96 ne = 84 npr = 93249 no. pairs analyzed = 93249 no. exposed pairs = 6082 no. arc points = 40353 no. surface atoms = 2078 nbur = 2526 mkacc time = 0.2000000 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 = 1.624000 m= 297 mr = 3864 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 4227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4028 ## 539 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 10472 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4658650E-10 1.3024946E-10 midg,1,midg; midg,igrid,midg 7.6554996E-10 2.1313179E-10 1,midg,midg; igrid,midg,midg 4.8508586E-10 1.6235682E-10 gauss-seidel spectral radius is 0.9810777 estimated iterations to convergence 60 setup time was (sec) 0.6400000 now iterating at: 03:10:28 rms-change max change #iterations 7.0486486E-02 12.21195 at 10iterations 6.4253486E-03 0.9647522 at 20iterations 1.8279591E-03 0.2613258 at 30iterations 6.7259604E-04 9.2174530E-02 at 40iterations 2.4981512E-04 3.3351898E-02 at 50iterations finished qdiffx linear iterations at : 03:10:30 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 2.4981512E-04 3.3351898E-02 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 03:10:31 3.217u 0.151s 0:03.64 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 Sun Oct 9 2011 at 03:10:31 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4604 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: 1.560217 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): 215.0780 276.0170 ymin,ymax (A): 71.70100 140.1530 zmin,zma (A): -70.09200 -6.305000 x,y,z range (A): 60.93901 68.45200 63.78700 scale (grids/A): 1.560217 object centre (A): 245.5475 105.9270 -38.19850 number of atom coordinates read : 4604 total number of charged atoms : 4429 net assigned charge : 18.49995 assigned positive charge : 682.1505 centred at (gu) : 93.86617 82.20266 92.69038 assigned negative charge : -663.6559 centred at (gu) : 94.10095 82.19891 92.93777 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 86392 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40353 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 26117 mr = 57639 m= 2494 mr = 17270 m= 55 mr = 1092 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 640 time to turn everything in is 0.6100000 number of dielectric boundary points 39057 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 495 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 33463 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) : 0.5200725 object centre at (A) : 245.5475 105.9270 -38.19850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5917960E-02 7.6316446E-03 midg,1,midg; midg,igrid,midg 3.5434064E-02 1.1968826E-02 1,midg,midg; igrid,midg,midg 8.8138944E-03 2.0722498E-03 gauss-seidel spectral radius is 0.9981699 estimated iterations to convergence 186 setup time was (sec) 0.8700000 now iterating at: 03:10:32 rms-change max change #iterations 3.781905 147.3669 at 10iterations 1.571659 54.19100 at 20iterations 0.6537308 23.51699 at 30iterations 0.2719956 9.444868 at 40iterations 0.1134450 3.639628 at 50iterations 4.7710843E-02 1.640327 at 60iterations 2.0303586E-02 0.6425762 at 70iterations 9.0796892E-03 0.2858772 at 80iterations 4.3601259E-03 0.1513271 at 90iterations 2.4368661E-03 8.1207275E-02 at 100iterations 1.5382105E-03 4.4094086E-02 at 110iterations 1.0445172E-03 2.9926300E-02 at 120iterations finished qdiffx linear iterations at : 03:10:38 total time elapsed so far: 6.880000 # loops : 120 mean,max change (kT/e) : 1.0445172E-03 2.9926300E-02 energy calculations done at 6.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.050000 DelPhi exited at 03:10:38 7.055u 0.144s 0:07.47 96.2% 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 Sun Oct 9 2011 at 03:10:38 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4604 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.340326 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): 215.0780 276.0170 ymin,ymax (A): 71.70100 140.1530 zmin,zma (A): -70.09200 -6.305000 x,y,z range (A): 60.93901 68.45200 63.78700 scale (grids/A): 2.340326 object centre (A): 245.5475 105.9270 -38.19850 number of atom coordinates read : 4604 total number of charged atoms : 4429 net assigned charge : 18.49995 assigned positive charge : 682.1505 centred at (gu) : 95.79864 78.30362 94.03515 assigned negative charge : -663.6559 centred at (gu) : 96.15134 78.29839 94.40662 start vw surface at 0.1900000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 200864 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40353 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 90318 mr = 141981 m= 25044 mr = 69312 m= 3701 mr = 18216 m= 217 mr = 2225 m= 2 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 2293 time to turn everything in is 1.440000 number of dielectric boundary points 88346 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 35346 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) : 1.560217 object centre at (A) : 245.5475 105.9270 -38.19850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5742885 9.4407521E-02 midg,1,midg; midg,igrid,midg 0.4887921 0.1818634 1,midg,midg; igrid,midg,midg 0.1707215 4.2903712E-03 gauss-seidel spectral radius is 0.9991751 estimated iterations to convergence 275 setup time was (sec) 1.720000 now iterating at: 03:10:40 rms-change max change #iterations 10.20121 327.6010 at 10iterations 5.915065 202.8882 at 20iterations 3.394104 77.71867 at 30iterations 1.939385 45.90528 at 40iterations 1.098155 23.70033 at 50iterations 0.6190583 13.34554 at 60iterations 0.3495334 7.404917 at 70iterations 0.1963129 4.844051 at 80iterations 0.1100602 2.110283 at 90iterations 6.1948664E-02 1.192044 at 100iterations 3.4789734E-02 0.6965008 at 110iterations 1.9563761E-02 0.4355354 at 120iterations 1.1082134E-02 0.2092209 at 130iterations 6.3485499E-03 0.1197243 at 140iterations 3.7199566E-03 7.8773499E-02 at 150iterations 2.2705263E-03 4.7519684E-02 at 160iterations 1.4591579E-03 2.9167175E-02 at 170iterations 9.9753076E-04 2.0370483E-02 at 180iterations finished qdiffx linear iterations at : 03:10:50 total time elapsed so far: 11.58000 # loops : 180 mean,max change (kT/e) : 9.9753076E-04 2.0370483E-02 energy calculations done at 11.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.75000 DelPhi exited at 03:10:51 11.753u 0.185s 0:12.29 97.0% 0+0k 0+0io 0pf+0w