Mon Oct 10 17:03:34 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 Mon Oct 10 2011 at 17:03:34 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2779 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: 0.5646312 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): -35.35500 9.116000 ymin,ymax (A): -31.81000 31.24000 zmin,zma (A): -24.11400 23.12400 x,y,z range (A): 44.47100 63.05000 47.23800 scale (grids/A): 0.5646312 object centre (A): -13.11950 -0.2849998 -0.4949999 number of atom coordinates read : 2779 total number of charged atoms : 2640 net assigned charge : -1.499972 assigned positive charge : 417.5732 centred at (gu) : 90.26146 90.15825 90.90375 assigned negative charge : -419.0743 centred at (gu) : 90.42647 90.11720 91.07053 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5846 nv = 96 ne = 84 npr = 54921 no. pairs analyzed = 54921 no. exposed pairs = 3661 no. arc points = 26013 no. surface atoms = 1227 nbur = 1552 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 = 1.540000 m= 243 mr = 2958 m= 1 mr = 12 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 0.3100000 number of dielectric boundary points 3120 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2688 ## 350 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7573 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4829654E-09 -2.8092266E-09 midg,1,midg; midg,igrid,midg -6.4167910E-10 3.5622311E-10 1,midg,midg; igrid,midg,midg 1.7144501E-09 -2.3755056E-09 gauss-seidel spectral radius is 0.9838065 estimated iterations to convergence 65 setup time was (sec) 0.5400000 now iterating at: 17:03:35 rms-change max change #iterations 8.4355541E-02 13.85880 at 10iterations 6.1624716E-03 1.138783 at 20iterations 4.4808743E-04 7.1728706E-02 at 30iterations 3.2329783E-05 5.9289932E-03 at 40iterations 2.4497599E-06 3.9291382E-04 at 50iterations finished qdiffx linear iterations at : 17:03:37 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 2.4497599E-06 3.9291382E-04 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 17:03:39 3.203u 0.156s 0:05.15 65.0% 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 Mon Oct 10 2011 at 17:03:39 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2779 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: 1.693894 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): -35.35500 9.116000 ymin,ymax (A): -31.81000 31.24000 zmin,zma (A): -24.11400 23.12400 x,y,z range (A): 44.47100 63.05000 47.23800 scale (grids/A): 1.693894 object centre (A): -13.11950 -0.2849998 -0.4949999 number of atom coordinates read : 2779 total number of charged atoms : 2640 net assigned charge : -1.499972 assigned positive charge : 417.5732 centred at (gu) : 90.78372 90.47394 92.71042 assigned negative charge : -419.0743 centred at (gu) : 91.27871 90.35168 93.21117 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 64660 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26013 grid for indexing accessible points = 1.400000 m= 19495 mr = 43110 m= 2018 mr = 13221 m= 48 mr = 1015 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 286 time to turn everything in is 0.4500000 number of dielectric boundary points 28870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 271 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 20359 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) : 0.5646312 object centre at (A) : -13.11950 -0.2849998 -0.4949999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0370388E-03 -1.9547487E-02 midg,1,midg; midg,igrid,midg 8.7882677E-04 5.5943695E-03 1,midg,midg; igrid,midg,midg 4.6866122E-03 -7.4123712E-03 gauss-seidel spectral radius is 0.9983001 estimated iterations to convergence 193 setup time was (sec) 0.7200000 now iterating at: 17:03:40 rms-change max change #iterations 3.488482 154.2305 at 10iterations 1.491791 57.21599 at 20iterations 0.6432235 23.45376 at 30iterations 0.2748787 10.82445 at 40iterations 0.1179129 4.405262 at 50iterations 5.0645821E-02 1.680621 at 60iterations 2.1693891E-02 0.7744102 at 70iterations 9.2971828E-03 0.3631086 at 80iterations 3.9793043E-03 0.1446915 at 90iterations 1.7124069E-03 6.4489365E-02 at 100iterations 7.3144125E-04 2.5673866E-02 at 110iterations 3.1522539E-04 1.1276245E-02 at 120iterations finished qdiffx linear iterations at : 17:03:46 total time elapsed so far: 6.680000 # loops : 120 mean,max change (kT/e) : 3.1522539E-04 1.1276245E-02 energy calculations done at 6.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.850000 DelPhi exited at 17:03:47 6.856u 0.170s 0:08.07 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 Mon Oct 10 2011 at 17:03:48 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2779 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.540841 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): -35.35500 9.116000 ymin,ymax (A): -31.81000 31.24000 zmin,zma (A): -24.11400 23.12400 x,y,z range (A): 44.47100 63.05000 47.23800 scale (grids/A): 2.540841 object centre (A): -13.11950 -0.2849998 -0.4949999 number of atom coordinates read : 2779 total number of charged atoms : 2640 net assigned charge : -1.499972 assigned positive charge : 417.5732 centred at (gu) : 91.17542 90.71076 94.06534 assigned negative charge : -419.0743 centred at (gu) : 91.91795 90.52747 94.81680 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 150057 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26013 grid for indexing accessible points = 1.400000 m= 67513 mr = 105576 m= 18958 mr = 52732 m= 3086 mr = 14203 m= 237 mr = 2070 m= 8 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 1072 time to turn everything in is 1.050000 number of dielectric boundary points 65183 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 21105 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) : 1.693894 object centre at (A) : -13.11950 -0.2849998 -0.4949999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.7669251E-02 -0.2393508 midg,1,midg; midg,igrid,midg 0.4274321 0.1027428 1,midg,midg; igrid,midg,midg 4.2638712E-02 -8.6616106E-02 gauss-seidel spectral radius is 0.9991782 estimated iterations to convergence 275 setup time was (sec) 1.330000 now iterating at: 17:03:49 rms-change max change #iterations 8.936986 328.9988 at 10iterations 5.077274 122.9610 at 20iterations 2.875403 74.27911 at 30iterations 1.618884 39.30860 at 40iterations 0.9091849 21.04732 at 50iterations 0.5095788 11.04104 at 60iterations 0.2854120 6.558100 at 70iterations 0.1595016 3.520443 at 80iterations 8.9135751E-02 1.979973 at 90iterations 4.9673464E-02 1.070827 at 100iterations 2.7710449E-02 0.5598793 at 110iterations 1.5393667E-02 0.2983494 at 120iterations 8.6023323E-03 0.1832161 at 130iterations 4.7954032E-03 9.7473145E-02 at 140iterations 2.6687649E-03 5.4728508E-02 at 150iterations 1.4861765E-03 2.9980898E-02 at 160iterations 8.2930946E-04 1.8199921E-02 at 170iterations 4.6141029E-04 9.7045898E-03 at 180iterations finished qdiffx linear iterations at : 17:04:00 total time elapsed so far: 11.61000 # loops : 180 mean,max change (kT/e) : 4.6141029E-04 9.7045898E-03 energy calculations done at 11.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.81000 DelPhi exited at 17:04:01 11.811u 0.225s 0:13.31 90.3% 0+0k 0+0io 0pf+0w