Tue Oct 11 08:34:17 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 Tue Oct 11 2011 at 08:34:17 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6619438 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): -10.44700 37.70000 ymin,ymax (A): -25.37300 22.80500 zmin,zma (A): -8.470000 45.31100 x,y,z range (A): 48.14700 48.17800 53.78100 scale (grids/A): 0.6619438 object centre (A): 13.62650 -1.283999 18.42050 number of atom coordinates read : 2734 total number of charged atoms : 2582 net assigned charge : 2.154014 assigned positive charge : 417.7339 centred at (gu) : 89.81448 90.12304 91.27560 assigned negative charge : -415.5803 centred at (gu) : 89.52959 89.92752 91.23308 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8011 nv = 96 ne = 84 npr = 55907 no. pairs analyzed = 55907 no. exposed pairs = 3298 no. arc points = 22958 no. surface atoms = 1110 nbur = 1624 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 476 mr = 4577 m= 1 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3200000 number of dielectric boundary points 3847 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2256 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9466 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7226066E-09 1.9924142E-08 midg,1,midg; midg,igrid,midg -3.7536722E-08 4.9704955E-08 1,midg,midg; igrid,midg,midg -6.1852113E-08 6.4746061E-08 gauss-seidel spectral radius is 0.9881800 estimated iterations to convergence 75 setup time was (sec) 0.6400000 now iterating at: 08:34:18 rms-change max change #iterations 0.1792209 22.66399 at 10iterations 1.9228624E-02 2.960603 at 20iterations 2.0737639E-03 0.2519913 at 30iterations 2.2867977E-04 2.9289246E-02 at 40iterations 2.5420446E-05 3.7574768E-03 at 50iterations finished qdiffx linear iterations at : 08:34:22 total time elapsed so far: 4.930000 # loops : 50 mean,max change (kT/e) : 2.5420446E-05 3.7574768E-03 energy calculations done at 4.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.090000 DelPhi exited at 08:34:23 5.097u 0.371s 0:05.77 94.6% 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 08:34:23 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.985831 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): -10.44700 37.70000 ymin,ymax (A): -25.37300 22.80500 zmin,zma (A): -8.470000 45.31100 x,y,z range (A): 48.14700 48.17800 53.78100 scale (grids/A): 1.985831 object centre (A): 13.62650 -1.283999 18.42050 number of atom coordinates read : 2734 total number of charged atoms : 2582 net assigned charge : 2.154014 assigned positive charge : 417.7339 centred at (gu) : 89.44296 90.36856 93.82626 assigned negative charge : -415.5803 centred at (gu) : 88.58848 89.78230 93.69902 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 85930 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22958 grid for indexing accessible points = 1.400000 m= 32415 mr = 60920 m= 5363 mr = 24201 m= 394 mr = 3437 m= 6 mr = 199 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 540 time to turn everything in is 0.6800000 number of dielectric boundary points 35351 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 20411 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) : 0.6619438 object centre at (A) : 13.62650 -1.283999 18.42050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5460776E-02 -3.7840900E-03 midg,1,midg; midg,igrid,midg -3.1760182E-02 3.3770401E-02 1,midg,midg; igrid,midg,midg -1.9460846E-02 7.9526894E-02 gauss-seidel spectral radius is 0.9987538 estimated iterations to convergence 224 setup time was (sec) 0.9900000 now iterating at: 08:34:24 rms-change max change #iterations 4.851190 199.6001 at 10iterations 2.353694 71.49500 at 20iterations 1.142828 35.24277 at 30iterations 0.5530876 18.19798 at 40iterations 0.2689717 7.522218 at 50iterations 0.1307468 3.927948 at 60iterations 6.3249454E-02 1.853988 at 70iterations 3.0642577E-02 0.8591967 at 80iterations 1.4960011E-02 0.4593430 at 90iterations 7.2232913E-03 0.2228718 at 100iterations 3.5167371E-03 9.6719742E-02 at 110iterations 1.7110724E-03 5.5965424E-02 at 120iterations finished qdiffx linear iterations at : 08:34:35 total time elapsed so far: 12.09000 # loops : 120 mean,max change (kT/e) : 1.7110724E-03 5.5965424E-02 energy calculations done at 12.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.24000 DelPhi exited at 08:34:36 12.246u 0.461s 0:13.12 96.7% 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 08:34:36 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.978747 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): -10.44700 37.70000 ymin,ymax (A): -25.37300 22.80500 zmin,zma (A): -8.470000 45.31100 x,y,z range (A): 48.14700 48.17800 53.78100 scale (grids/A): 2.978747 object centre (A): 13.62650 -1.283999 18.42050 number of atom coordinates read : 2734 total number of charged atoms : 2582 net assigned charge : 2.154014 assigned positive charge : 417.7339 centred at (gu) : 89.16437 90.55264 95.73929 assigned negative charge : -415.5803 centred at (gu) : 87.88265 89.67349 95.54847 start vw surface at 0.1200000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 198504 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22958 grid for indexing accessible points = 1.400000 m= 103435 mr = 146855 m= 38952 mr = 85614 m= 9831 mr = 31605 m= 1616 mr = 7544 m= 162 mr = 1166 m= 2 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 1782 time to turn everything in is 1.850000 number of dielectric boundary points 79621 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 20651 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) : 1.985831 object centre at (A) : 13.62650 -1.283999 18.42050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4642275 0.1097507 midg,1,midg; midg,igrid,midg -0.3305835 0.3991759 1,midg,midg; igrid,midg,midg -0.1226707 0.6863683 gauss-seidel spectral radius is 0.9992865 estimated iterations to convergence 295 setup time was (sec) 2.190000 now iterating at: 08:34:38 rms-change max change #iterations 11.04499 413.0633 at 10iterations 6.487280 146.0063 at 20iterations 3.802278 84.38080 at 30iterations 2.228472 45.16367 at 40iterations 1.303836 25.96173 at 50iterations 0.7613715 13.15668 at 60iterations 0.4443231 7.504327 at 70iterations 0.2591798 4.539747 at 80iterations 0.1510177 2.498913 at 90iterations 8.8020593E-02 1.579517 at 100iterations 5.1119078E-02 0.9032955 at 110iterations 2.9803880E-02 0.5232506 at 120iterations 1.7349442E-02 0.2861404 at 130iterations 1.0086496E-02 0.1605406 at 140iterations 5.8837989E-03 9.8882198E-02 at 150iterations 3.4303290E-03 5.7048798E-02 at 160iterations 2.0058833E-03 3.2773972E-02 at 170iterations 1.1768413E-03 1.9989014E-02 at 180iterations finished qdiffx linear iterations at : 08:34:56 total time elapsed so far: 20.07000 # loops : 180 mean,max change (kT/e) : 1.1768413E-03 1.9989014E-02 energy calculations done at 20.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.23000 DelPhi exited at 08:34:57 20.231u 0.474s 0:21.09 98.1% 0+0k 0+0io 0pf+0w