Tue Oct 11 06:49:27 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+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 06:49:28 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2954 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5566589 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): -18.42700 45.52600 ymin,ymax (A): 21.54200 78.69500 zmin,zma (A): -72.27100 -23.16800 x,y,z range (A): 63.95300 57.15300 49.10300 scale (grids/A): 0.5566589 object centre (A): 13.54950 50.11850 -47.71950 number of atom coordinates read : 2954 total number of charged atoms : 2812 net assigned charge : -2.460990 assigned positive charge : 432.1367 centred at (gu) : 88.92391 89.72158 90.00327 assigned negative charge : -434.5983 centred at (gu) : 88.90521 89.80746 89.98911 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5923 nv = 96 ne = 84 npr = 61018 no. pairs analyzed = 61018 no. exposed pairs = 3675 no. arc points = 25742 no. surface atoms = 1243 nbur = 1711 mkacc time = 0.1300000 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 = 1.540000 m= 230 mr = 3143 m= 0 mr = 20 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3200000 number of dielectric boundary points 2990 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2541 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7704 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6676800E-10 -9.5090914E-11 midg,1,midg; midg,igrid,midg 6.2806726E-10 -9.9449227E-10 1,midg,midg; igrid,midg,midg -5.3332994E-10 -4.1822611E-11 gauss-seidel spectral radius is 0.9833546 estimated iterations to convergence 64 setup time was (sec) 0.5200000 now iterating at: 06:49:28 rms-change max change #iterations 8.0368936E-02 12.60302 at 10iterations 5.6621768E-03 0.8841553 at 20iterations 4.2156017E-04 7.2505951E-02 at 30iterations 4.4821896E-05 1.0591507E-02 at 40iterations 8.1046155E-06 2.0055771E-03 at 50iterations finished qdiffx linear iterations at : 06:49:31 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 8.1046155E-06 2.0055771E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 06:49:31 3.084u 0.148s 0:03.78 85.1% 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 06:49:31 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2954 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.669976 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): -18.42700 45.52600 ymin,ymax (A): 21.54200 78.69500 zmin,zma (A): -72.27100 -23.16800 x,y,z range (A): 63.95300 57.15300 49.10300 scale (grids/A): 1.669976 object centre (A): 13.54950 50.11850 -47.71950 number of atom coordinates read : 2954 total number of charged atoms : 2812 net assigned charge : -2.460990 assigned positive charge : 432.1367 centred at (gu) : 86.77095 89.16417 90.00942 assigned negative charge : -434.5983 centred at (gu) : 86.71555 89.42205 89.96660 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 65936 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25742 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20833 mr = 45019 m= 2279 mr = 14818 m= 54 mr = 1285 m= 0 mr = 9 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1199 time to turn everything in is 0.4600000 number of dielectric boundary points 27971 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 241 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 21638 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) : 0.5566589 object centre at (A) : 13.54950 50.11850 -47.71950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7668405E-03 9.8155728E-03 midg,1,midg; midg,igrid,midg -1.9999135E-03 6.2624542E-03 1,midg,midg; igrid,midg,midg -1.6714744E-02 -3.2036915E-02 gauss-seidel spectral radius is 0.9982665 estimated iterations to convergence 191 setup time was (sec) 0.7200000 now iterating at: 06:49:32 rms-change max change #iterations 3.432964 150.1301 at 10iterations 1.460807 58.45785 at 20iterations 0.6206095 24.33032 at 30iterations 0.2640666 9.032139 at 40iterations 0.1129125 4.070884 at 50iterations 4.8057292E-02 1.660286 at 60iterations 2.0351544E-02 0.6681499 at 70iterations 8.6672483E-03 0.2811291 at 80iterations 3.7020021E-03 0.1280060 at 90iterations 1.5757275E-03 5.2579880E-02 at 100iterations 6.7214819E-04 2.4930000E-02 at 110iterations 2.8725906E-04 1.0177612E-02 at 120iterations finished qdiffx linear iterations at : 06:49:38 total time elapsed so far: 6.630000 # loops : 120 mean,max change (kT/e) : 2.8725906E-04 1.0177612E-02 energy calculations done at 6.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.810000 DelPhi exited at 06:49:39 6.811u 0.149s 0:07.43 93.5% 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 06:49:39 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2954 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.504965 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): -18.42700 45.52600 ymin,ymax (A): 21.54200 78.69500 zmin,zma (A): -72.27100 -23.16800 x,y,z range (A): 63.95300 57.15300 49.10300 scale (grids/A): 2.504965 object centre (A): 13.54950 50.11850 -47.71950 number of atom coordinates read : 2954 total number of charged atoms : 2812 net assigned charge : -2.460990 assigned positive charge : 432.1367 centred at (gu) : 85.15630 88.74619 90.01420 assigned negative charge : -434.5983 centred at (gu) : 85.07321 89.13316 89.94998 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 152872 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25742 grid for indexing accessible points = 1.400000 m= 71444 mr = 109767 m= 21322 mr = 57483 m= 3688 mr = 16591 m= 302 mr = 2655 m= 5 mr = 146 m= 0 mr = 0 time to grow re-entrant surface = 0.5899999 no. cavity mid-points inaccessible to solvent = 4085 time to turn everything in is 1.060000 number of dielectric boundary points 62991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 22481 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) : 1.669976 object centre at (A) : 13.54950 50.11850 -47.71950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.2610838E-02 0.1601892 midg,1,midg; midg,igrid,midg -3.5698354E-02 0.1267831 1,midg,midg; igrid,midg,midg -0.2554776 -0.7978700 gauss-seidel spectral radius is 0.9991646 estimated iterations to convergence 273 setup time was (sec) 1.330000 now iterating at: 06:49:40 rms-change max change #iterations 8.760602 282.5230 at 10iterations 4.923478 110.6738 at 20iterations 2.767325 63.77423 at 30iterations 1.552052 32.24129 at 40iterations 0.8645448 17.62117 at 50iterations 0.4829595 10.01843 at 60iterations 0.2681007 5.350748 at 70iterations 0.1493678 3.300288 at 80iterations 8.2913369E-02 1.599209 at 90iterations 4.5967985E-02 0.9507236 at 100iterations 2.5466792E-02 0.5348873 at 110iterations 1.4116482E-02 0.2799311 at 120iterations 7.8467885E-03 0.1661825 at 130iterations 4.3545631E-03 8.6720943E-02 at 140iterations 2.4141453E-03 5.2682877E-02 at 150iterations 1.3403363E-03 2.7954102E-02 at 160iterations 7.4465462E-04 1.4710426E-02 at 170iterations 4.1367154E-04 8.6708069E-03 at 180iterations finished qdiffx linear iterations at : 06:49:49 total time elapsed so far: 10.43000 # loops : 180 mean,max change (kT/e) : 4.1367154E-04 8.6708069E-03 energy calculations done at 10.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.60000 DelPhi exited at 06:49:51 10.604u 0.187s 0:11.83 91.1% 0+0k 0+0io 0pf+0w