Sat Oct 8 16:11:44 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 16:11:44 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2410 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: HIR 874 has a net charge of 0.5140 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: 0.5898044 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): -2.880000 47.47400 ymin,ymax (A): -16.59200 29.26700 zmin,zma (A): -18.32800 42.03100 x,y,z range (A): 50.35400 45.85900 60.35900 scale (grids/A): 0.5898044 object centre (A): 22.29700 6.337500 11.85150 number of atom coordinates read : 2410 total number of charged atoms : 2310 net assigned charge : 2.914002 assigned positive charge : 359.5859 centred at (gu) : 89.72619 88.94210 88.83350 assigned negative charge : -356.6727 centred at (gu) : 89.74905 89.03959 88.88323 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5420 nv = 96 ne = 84 npr = 49883 no. pairs analyzed = 49883 no. exposed pairs = 2950 no. arc points = 20738 no. surface atoms = 1005 nbur = 1405 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 = 1.456000 m= 240 mr = 2907 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2800000 number of dielectric boundary points 2741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2133 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6962 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6773970E-09 -2.7233260E-10 midg,1,midg; midg,igrid,midg 4.0732804E-09 -1.2012848E-09 1,midg,midg; igrid,midg,midg 1.4874199E-09 2.7279323E-10 gauss-seidel spectral radius is 0.9851085 estimated iterations to convergence 67 setup time was (sec) 0.5900000 now iterating at: 16:11:45 rms-change max change #iterations 9.3219839E-02 15.06070 at 10iterations 7.4880761E-03 1.160096 at 20iterations 6.1457936E-04 0.1041393 at 30iterations 5.2810981E-05 9.3879700E-03 at 40iterations 5.3987255E-06 8.4590912E-04 at 50iterations finished qdiffx linear iterations at : 16:11:48 total time elapsed so far: 4.390000 # loops : 50 mean,max change (kT/e) : 5.3987255E-06 8.4590912E-04 energy calculations done at 4.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.540000 DelPhi exited at 16:11:49 4.544u 0.413s 0:05.24 94.4% 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 16:11:49 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2410 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: HIR 874 has a net charge of 0.5140 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: 1.769413 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): -2.880000 47.47400 ymin,ymax (A): -16.59200 29.26700 zmin,zma (A): -18.32800 42.03100 x,y,z range (A): 50.35400 45.85900 60.35900 scale (grids/A): 1.769413 object centre (A): 22.29700 6.337500 11.85150 number of atom coordinates read : 2410 total number of charged atoms : 2310 net assigned charge : 2.914002 assigned positive charge : 359.5859 centred at (gu) : 89.17783 86.82571 86.50018 assigned negative charge : -356.6727 centred at (gu) : 89.24693 87.11864 86.64948 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 59606 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20738 grid for indexing accessible points = 1.400000 m= 18984 mr = 40992 m= 2406 mr = 13393 m= 77 mr = 1389 m= 0 mr = 12 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1320 time to turn everything in is 0.4800000 number of dielectric boundary points 25287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 189 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 18001 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) : 0.5898044 object centre at (A) : 22.29700 6.337500 11.85150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0528672E-02 1.4508792E-02 midg,1,midg; midg,igrid,midg 9.7914785E-03 -2.8400526E-03 1,midg,midg; igrid,midg,midg 7.2035909E-04 -2.0516057E-02 gauss-seidel spectral radius is 0.9983985 estimated iterations to convergence 198 setup time was (sec) 0.7700000 now iterating at: 16:11:50 rms-change max change #iterations 3.514900 206.0511 at 10iterations 1.545147 62.75987 at 20iterations 0.6782920 24.62365 at 30iterations 0.2998033 11.75641 at 40iterations 0.1316126 5.047703 at 50iterations 5.7975311E-02 2.071213 at 60iterations 2.5485938E-02 0.8912654 at 70iterations 1.1232062E-02 0.3851409 at 80iterations 4.9277269E-03 0.1688194 at 90iterations 2.1750992E-03 7.6035023E-02 at 100iterations 9.5943024E-04 3.7430763E-02 at 110iterations 4.2118484E-04 1.4598846E-02 at 120iterations finished qdiffx linear iterations at : 16:11:59 total time elapsed so far: 9.990000 # loops : 120 mean,max change (kT/e) : 4.2118484E-04 1.4598846E-02 energy calculations done at 9.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.17000 DelPhi exited at 16:12:00 10.175u 0.445s 0:10.90 97.3% 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 16:12:00 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2410 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: HIR 874 has a net charge of 0.5140 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: 2.654119 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): -2.880000 47.47400 ymin,ymax (A): -16.59200 29.26700 zmin,zma (A): -18.32800 42.03100 x,y,z range (A): 50.35400 45.85900 60.35900 scale (grids/A): 2.654119 object centre (A): 22.29700 6.337500 11.85150 number of atom coordinates read : 2410 total number of charged atoms : 2310 net assigned charge : 2.914002 assigned positive charge : 359.5859 centred at (gu) : 88.76669 85.23849 84.75016 assigned negative charge : -356.6727 centred at (gu) : 88.87031 85.67793 84.97415 start vw surface at 0.1200000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 138403 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20738 grid for indexing accessible points = 1.400000 m= 64047 mr = 99872 m= 20140 mr = 51232 m= 4122 mr = 15747 m= 351 mr = 2953 m= 13 mr = 177 m= 0 mr = 2 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 4427 time to turn everything in is 1.220000 number of dielectric boundary points 57093 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 18474 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) : 1.769413 object centre at (A) : 22.29700 6.337500 11.85150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2397521 0.4353620 midg,1,midg; midg,igrid,midg 9.9334389E-02 -4.5547802E-02 1,midg,midg; igrid,midg,midg 1.2586880E-02 -0.3505049 gauss-seidel spectral radius is 0.9991877 estimated iterations to convergence 277 setup time was (sec) 1.540000 now iterating at: 16:12:02 rms-change max change #iterations 8.626733 306.1922 at 10iterations 4.912913 161.8385 at 20iterations 2.790692 68.13747 at 30iterations 1.579611 39.05272 at 40iterations 0.8893490 19.25000 at 50iterations 0.5015046 10.45718 at 60iterations 0.2812410 5.967812 at 70iterations 0.1582467 3.419309 at 80iterations 8.8905752E-02 1.960724 at 90iterations 4.9855903E-02 1.103646 at 100iterations 2.7892997E-02 0.6535234 at 110iterations 1.5672555E-02 0.3491974 at 120iterations 8.7762224E-03 0.2033386 at 130iterations 4.9135992E-03 9.5371246E-02 at 140iterations 2.7476088E-03 5.5819035E-02 at 150iterations 1.5377012E-03 3.2570839E-02 at 160iterations 8.6214504E-04 1.8409729E-02 at 170iterations 4.8314015E-04 9.7789764E-03 at 180iterations finished qdiffx linear iterations at : 16:12:18 total time elapsed so far: 17.44000 # loops : 180 mean,max change (kT/e) : 4.8314015E-04 9.7789764E-03 energy calculations done at 17.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.61000 DelPhi exited at 16:12:18 17.618u 0.443s 0:18.35 98.3% 0+0k 0+0io 0pf+0w