Mon Oct 10 17:11:17 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+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 Mon Oct 10 2011 at 17:11:17 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3009 !!! WARNING: HIZ 617 has a net charge of 0.2000 !!! WARNING: HIZ 653 has a net charge of 0.2000 !!! WARNING: MG8 861 has a net charge of 1.4000 !!! WARNING: ZN8 862 has a net charge of 1.4000 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: 0.6265290 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): 48.50700 101.5160 ymin,ymax (A): -7.218000 49.60300 zmin,zma (A): -5.360000 47.96100 x,y,z range (A): 53.00900 56.82100 53.32100 scale (grids/A): 0.6265290 object centre (A): 75.01150 21.19250 21.30050 number of atom coordinates read : 3009 total number of charged atoms : 2867 net assigned charge : 5.700033 assigned positive charge : 458.5969 centred at (gu) : 89.04231 89.28873 90.86801 assigned negative charge : -452.8983 centred at (gu) : 89.06139 89.35015 91.00391 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7691 nv = 96 ne = 84 npr = 61426 no. pairs analyzed = 61426 no. exposed pairs = 3792 no. arc points = 26627 no. surface atoms = 1275 nbur = 1734 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 429 mr = 4136 m= 0 mr = 32 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2646 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9555 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5024819E-08 -8.8577483E-09 midg,1,midg; midg,igrid,midg 1.3243281E-08 -6.7269121E-11 1,midg,midg; igrid,midg,midg 9.1232470E-09 3.1764642E-09 gauss-seidel spectral radius is 0.9868414 estimated iterations to convergence 71 setup time was (sec) 0.5300000 now iterating at: 17:11:17 rms-change max change #iterations 0.1444277 21.94682 at 10iterations 1.3766221E-02 2.206051 at 20iterations 1.3566371E-03 0.1784759 at 30iterations 1.7271456E-04 2.3102760E-02 at 40iterations 3.6202484E-05 5.2099228E-03 at 50iterations finished qdiffx linear iterations at : 17:11:20 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 3.6202484E-05 5.2099228E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 17:11:20 3.125u 0.133s 0:03.57 91.0% 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 17:11:20 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3009 !!! WARNING: HIZ 617 has a net charge of 0.2000 !!! WARNING: HIZ 653 has a net charge of 0.2000 !!! WARNING: MG8 861 has a net charge of 1.4000 !!! WARNING: ZN8 862 has a net charge of 1.4000 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: 1.879587 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): 48.50700 101.5160 ymin,ymax (A): -7.218000 49.60300 zmin,zma (A): -5.360000 47.96100 x,y,z range (A): 53.00900 56.82100 53.32100 scale (grids/A): 1.879587 object centre (A): 75.01150 21.19250 21.30050 number of atom coordinates read : 3009 total number of charged atoms : 2867 net assigned charge : 5.700033 assigned positive charge : 458.5969 centred at (gu) : 87.12598 87.86584 92.60302 assigned negative charge : -452.8983 centred at (gu) : 87.18398 88.05024 93.01109 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 83948 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26627 grid for indexing accessible points = 1.400000 m= 29592 mr = 57651 m= 4768 mr = 21269 m= 289 mr = 2897 m= 5 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 187 time to turn everything in is 0.5800000 number of dielectric boundary points 36685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 190 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 22509 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) : 0.6265290 object centre at (A) : 75.01150 21.19250 21.30050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5222327E-02 -4.1973488E-03 midg,1,midg; midg,igrid,midg 1.4954500E-02 8.8824155E-03 1,midg,midg; igrid,midg,midg 1.1888911E-02 1.8792389E-03 gauss-seidel spectral radius is 0.9986418 estimated iterations to convergence 215 setup time was (sec) 0.8400000 now iterating at: 17:11:21 rms-change max change #iterations 4.595254 203.6940 at 10iterations 2.148936 72.41890 at 20iterations 1.011199 31.15915 at 30iterations 0.4739029 14.19458 at 40iterations 0.2215790 7.080212 at 50iterations 0.1043592 3.224234 at 60iterations 4.9121782E-02 1.500408 at 70iterations 2.3038870E-02 0.7485065 at 80iterations 1.0823762E-02 0.3383808 at 90iterations 5.0849561E-03 0.1677990 at 100iterations 2.3938611E-03 6.9370270E-02 at 110iterations 1.1280897E-03 3.3222198E-02 at 120iterations finished qdiffx linear iterations at : 17:11:27 total time elapsed so far: 6.890000 # loops : 120 mean,max change (kT/e) : 1.1280897E-03 3.3222198E-02 energy calculations done at 6.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.060000 DelPhi exited at 17:11:28 7.059u 0.166s 0:07.61 94.7% 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 Mon Oct 10 2011 at 17:11:28 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3009 !!! WARNING: HIZ 617 has a net charge of 0.2000 !!! WARNING: HIZ 653 has a net charge of 0.2000 !!! WARNING: MG8 861 has a net charge of 1.4000 !!! WARNING: ZN8 862 has a net charge of 1.4000 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: 2.819380 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): 48.50700 101.5160 ymin,ymax (A): -7.218000 49.60300 zmin,zma (A): -5.360000 47.96100 x,y,z range (A): 53.00900 56.82100 53.32100 scale (grids/A): 2.819380 object centre (A): 75.01150 21.19250 21.30050 number of atom coordinates read : 3009 total number of charged atoms : 2867 net assigned charge : 5.700033 assigned positive charge : 458.5969 centred at (gu) : 85.68886 86.79851 93.90427 assigned negative charge : -452.8983 centred at (gu) : 85.77575 87.07522 94.51662 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 194853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26627 grid for indexing accessible points = 1.400000 m= 95361 mr = 140846 m= 34858 mr = 76659 m= 8601 mr = 27436 m= 1271 mr = 6312 m= 65 mr = 848 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 594 time to turn everything in is 1.440000 number of dielectric boundary points 82892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 22936 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) : 1.879587 object centre at (A) : 75.01150 21.19250 21.30050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5393798 3.8973048E-02 midg,1,midg; midg,igrid,midg 0.1470441 0.2285527 1,midg,midg; igrid,midg,midg 0.1221637 7.0428676E-03 gauss-seidel spectral radius is 0.9992726 estimated iterations to convergence 293 setup time was (sec) 1.720000 now iterating at: 17:11:30 rms-change max change #iterations 10.79344 374.2158 at 10iterations 6.398892 152.1256 at 20iterations 3.750388 80.45036 at 30iterations 2.194312 41.82886 at 40iterations 1.281280 27.94665 at 50iterations 0.7455379 14.12739 at 60iterations 0.4336534 8.714267 at 70iterations 0.2515272 4.415619 at 80iterations 0.1458697 2.533721 at 90iterations 8.4420934E-02 1.427997 at 100iterations 4.8894331E-02 0.8268948 at 110iterations 2.8330972E-02 0.5192575 at 120iterations 1.6372230E-02 0.2928802 at 130iterations 9.4821556E-03 0.1627731 at 140iterations 5.4938085E-03 8.8568687E-02 at 150iterations 3.1787492E-03 5.4731369E-02 at 160iterations 1.8403265E-03 3.4896851E-02 at 170iterations 1.0719334E-03 2.1266937E-02 at 180iterations finished qdiffx linear iterations at : 17:11:40 total time elapsed so far: 11.91000 # loops : 180 mean,max change (kT/e) : 1.0719334E-03 2.1266937E-02 energy calculations done at 11.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.08000 DelPhi exited at 17:11:41 12.085u 0.223s 0:12.61 97.5% 0+0k 0+0io 0pf+0w