Tue Oct 11 06:36:56 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 Tue Oct 11 2011 at 06:36:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2071 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: 0.7102669 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): -20.68500 24.64500 ymin,ymax (A): -28.56900 11.08300 zmin,zma (A): -13.47200 36.65000 x,y,z range (A): 45.33000 39.65200 50.12200 scale (grids/A): 0.7102669 object centre (A): 1.980000 -8.743000 11.58900 number of atom coordinates read : 2071 total number of charged atoms : 1949 net assigned charge : 6.500009 assigned positive charge : 315.1740 centred at (gu) : 90.15751 90.64005 89.23270 assigned negative charge : -308.6742 centred at (gu) : 90.01485 90.62029 89.15819 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7080 nv = 96 ne = 84 npr = 41804 no. pairs analyzed = 41804 no. exposed pairs = 2495 no. arc points = 16855 no. surface atoms = 854 nbur = 1217 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 457 mr = 4087 m= 9 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3380 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1703 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7943 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2338709E-08 8.4020833E-08 midg,1,midg; midg,igrid,midg 4.3088683E-08 7.7955150E-08 1,midg,midg; igrid,midg,midg -1.5933262E-08 1.3609285E-07 gauss-seidel spectral radius is 0.9896634 estimated iterations to convergence 80 setup time was (sec) 0.4600000 now iterating at: 06:36:57 rms-change max change #iterations 0.2029507 28.59024 at 10iterations 2.5737135E-02 3.498952 at 20iterations 3.3783726E-03 0.4469299 at 30iterations 5.2343175E-04 7.4440002E-02 at 40iterations 1.2265673E-04 1.8898010E-02 at 50iterations finished qdiffx linear iterations at : 06:36:59 total time elapsed so far: 2.850000 # loops : 50 mean,max change (kT/e) : 1.2265673E-04 1.8898010E-02 energy calculations done at 2.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.020000 DelPhi exited at 06:37:00 3.024u 0.140s 0:03.55 89.0% 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 Tue Oct 11 2011 at 06:37:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2071 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: 2.130801 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): -20.68500 24.64500 ymin,ymax (A): -28.56900 11.08300 zmin,zma (A): -13.47200 36.65000 x,y,z range (A): 45.33000 39.65200 50.12200 scale (grids/A): 2.130801 object centre (A): 1.980000 -8.743000 11.58900 number of atom coordinates read : 2071 total number of charged atoms : 1949 net assigned charge : 6.500009 assigned positive charge : 315.1740 centred at (gu) : 90.47258 91.92022 87.69810 assigned negative charge : -308.6742 centred at (gu) : 90.04436 91.86101 87.47472 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 75122 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16855 grid for indexing accessible points = 1.400000 m= 29937 mr = 53667 m= 5752 mr = 22762 m= 538 mr = 3782 m= 11 mr = 286 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 30863 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 15471 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) : 0.7102669 object centre at (A) : 1.980000 -8.743000 11.58900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3805515E-02 4.5003250E-02 midg,1,midg; midg,igrid,midg 6.0369195E-03 3.4463938E-02 1,midg,midg; igrid,midg,midg 1.6583953E-02 3.6190175E-02 gauss-seidel spectral radius is 0.9988366 estimated iterations to convergence 232 setup time was (sec) 0.8600000 now iterating at: 06:37:01 rms-change max change #iterations 4.582327 178.5659 at 10iterations 2.273257 72.06461 at 20iterations 1.132147 33.25027 at 30iterations 0.5622646 18.02580 at 40iterations 0.2796217 9.111298 at 50iterations 0.1395427 4.128229 at 60iterations 6.9414817E-02 2.118195 at 70iterations 3.4529187E-02 1.099401 at 80iterations 1.7235374E-02 0.5025711 at 90iterations 8.6306501E-03 0.2647982 at 100iterations 4.3223300E-03 0.1292877 at 110iterations 2.1974188E-03 6.8258286E-02 at 120iterations finished qdiffx linear iterations at : 06:37:08 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 2.1974188E-03 6.8258286E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 06:37:08 7.804u 0.241s 0:08.61 93.3% 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 Tue Oct 11 2011 at 06:37:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2071 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: 3.196201 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): -20.68500 24.64500 ymin,ymax (A): -28.56900 11.08300 zmin,zma (A): -13.47200 36.65000 x,y,z range (A): 45.33000 39.65200 50.12200 scale (grids/A): 3.196201 object centre (A): 1.980000 -8.743000 11.58900 number of atom coordinates read : 2071 total number of charged atoms : 1949 net assigned charge : 6.500009 assigned positive charge : 315.1740 centred at (gu) : 90.70882 92.88023 86.54714 assigned negative charge : -308.6742 centred at (gu) : 90.06664 92.79143 86.21210 start vw surface at 0.1300000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 173168 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16855 grid for indexing accessible points = 1.400000 m= 93709 mr = 129070 m= 37765 mr = 77985 m= 10832 mr = 31171 m= 2186 mr = 8346 m= 271 mr = 1592 m= 12 mr = 188 m= 0 mr = 4 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.750000 number of dielectric boundary points 69587 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 15592 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) : 2.130801 object centre at (A) : 1.980000 -8.743000 11.58900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5871213 0.3760430 midg,1,midg; midg,igrid,midg 1.7800087E-02 0.2702935 1,midg,midg; igrid,midg,midg 0.2859746 0.2824368 gauss-seidel spectral radius is 0.9992939 estimated iterations to convergence 297 setup time was (sec) 2.060000 now iterating at: 06:37:11 rms-change max change #iterations 10.18538 383.9132 at 10iterations 6.012106 118.5510 at 20iterations 3.554866 81.23062 at 30iterations 2.090721 37.43038 at 40iterations 1.228464 22.84661 at 50iterations 0.7206995 13.05524 at 60iterations 0.4237228 8.188227 at 70iterations 0.2476814 4.403269 at 80iterations 0.1450332 2.702262 at 90iterations 8.5016236E-02 1.633306 at 100iterations 4.9835235E-02 0.8388443 at 110iterations 2.9314075E-02 0.5431099 at 120iterations 1.7266575E-02 0.3302822 at 130iterations 1.0311592E-02 0.1688232 at 140iterations 6.2553654E-03 0.1286240 at 150iterations 3.8937535E-03 7.4926376E-02 at 160iterations 2.5464823E-03 4.7039032E-02 at 170iterations 1.7537508E-03 3.2123566E-02 at 180iterations finished qdiffx linear iterations at : 06:37:21 total time elapsed so far: 12.72000 # loops : 180 mean,max change (kT/e) : 1.7537508E-03 3.2123566E-02 energy calculations done at 12.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 06:37:22 12.898u 0.277s 0:13.54 97.1% 0+0k 0+0io 0pf+0w