Sat Oct 15 12:01:28 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 Sat Oct 15 2011 at 12:01:28 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2162 !!! WARNING: HIT 84 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6850896 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): 0.7310001 52.69500 ymin,ymax (A): -15.22300 27.67800 zmin,zma (A): -11.48100 39.68800 x,y,z range (A): 51.96400 42.90100 51.16900 scale (grids/A): 0.6850896 object centre (A): 26.71300 6.227500 14.10350 number of atom coordinates read : 2162 total number of charged atoms : 2028 net assigned charge : 9.514021 assigned positive charge : 316.5868 centred at (gu) : 89.44154 88.59056 91.42389 assigned negative charge : -307.0733 centred at (gu) : 89.44180 88.68683 91.38979 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7023 nv = 96 ne = 84 npr = 43317 no. pairs analyzed = 43317 no. exposed pairs = 2796 no. arc points = 20215 no. surface atoms = 939 nbur = 1223 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 462 mr = 3764 m= 3 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 56 time to turn everything in is 0.1800000 number of dielectric boundary points 3653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1858 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7895 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7402042E-08 7.3634219E-08 midg,1,midg; midg,igrid,midg 9.7215839E-08 1.3782445E-08 1,midg,midg; igrid,midg,midg 5.1076096E-08 4.1020265E-08 gauss-seidel spectral radius is 0.9889214 estimated iterations to convergence 77 setup time was (sec) 0.3800000 now iterating at: 12:01:29 rms-change max change #iterations 0.1795174 26.49399 at 10iterations 2.0246716E-02 3.032761 at 20iterations 2.3507522E-03 0.3536549 at 30iterations 2.7396114E-04 3.9276123E-02 at 40iterations 3.1617532E-05 4.3563843E-03 at 50iterations finished qdiffx linear iterations at : 12:01:32 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 3.1617532E-05 4.3563843E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 12:01:32 3.444u 0.163s 0:03.88 92.7% 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 Sat Oct 15 2011 at 12:01:32 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2162 !!! WARNING: HIT 84 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.055269 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): 0.7310001 52.69500 ymin,ymax (A): -15.22300 27.67800 zmin,zma (A): -11.48100 39.68800 x,y,z range (A): 51.96400 42.90100 51.16900 scale (grids/A): 2.055269 object centre (A): 26.71300 6.227500 14.10350 number of atom coordinates read : 2162 total number of charged atoms : 2028 net assigned charge : 9.514021 assigned positive charge : 316.5868 centred at (gu) : 88.32448 85.77168 94.27142 assigned negative charge : -307.0733 centred at (gu) : 88.32559 86.06042 94.16943 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 74125 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20215 grid for indexing accessible points = 1.400000 m= 28119 mr = 49873 m= 5249 mr = 20733 m= 444 mr = 3365 m= 3 mr = 207 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 2318 time to turn everything in is 0.3700000 number of dielectric boundary points 33762 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 99 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 16071 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) : 0.6850896 object centre at (A) : 26.71300 6.227500 14.10350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8167383E-02 3.8180016E-02 midg,1,midg; midg,igrid,midg 3.4735493E-02 -6.6492325E-03 1,midg,midg; igrid,midg,midg 6.5813951E-02 6.8367474E-02 gauss-seidel spectral radius is 0.9987815 estimated iterations to convergence 227 setup time was (sec) 0.6000000 now iterating at: 12:01:33 rms-change max change #iterations 4.310031 177.9387 at 10iterations 2.091761 80.79254 at 20iterations 1.017148 34.90527 at 30iterations 0.4950099 16.03673 at 40iterations 0.2407646 7.581196 at 50iterations 0.1174306 3.564421 at 60iterations 5.7562593E-02 2.217841 at 70iterations 2.7942365E-02 0.9476417 at 80iterations 1.3594990E-02 0.4135742 at 90iterations 6.6295140E-03 0.2048259 at 100iterations 3.2410352E-03 0.1107635 at 110iterations 1.5829486E-03 4.6718597E-02 at 120iterations finished qdiffx linear iterations at : 12:01:40 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 1.5829486E-03 4.6718597E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 12:01:41 7.981u 0.208s 0:08.61 95.0% 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 Sat Oct 15 2011 at 12:01:41 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2162 !!! WARNING: HIT 84 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.082904 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): 0.7310001 52.69500 ymin,ymax (A): -15.22300 27.67800 zmin,zma (A): -11.48100 39.68800 x,y,z range (A): 51.96400 42.90100 51.16900 scale (grids/A): 3.082904 object centre (A): 26.71300 6.227500 14.10350 number of atom coordinates read : 2162 total number of charged atoms : 2028 net assigned charge : 9.514021 assigned positive charge : 316.5868 centred at (gu) : 87.48657 83.65746 96.40702 assigned negative charge : -307.0733 centred at (gu) : 87.48839 84.09074 96.25426 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 170872 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20215 grid for indexing accessible points = 1.400000 m= 87805 mr = 120859 m= 35049 mr = 71483 m= 9742 mr = 28194 m= 1807 mr = 7437 m= 138 mr = 1302 m= 1 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 7513 time to turn everything in is 1.120000 number of dielectric boundary points 76066 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 16220 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) : 2.055269 object centre at (A) : 26.71300 6.227500 14.10350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7055130 0.3978049 midg,1,midg; midg,igrid,midg 0.2870954 -4.8929758E-02 1,midg,midg; igrid,midg,midg 0.5077707 0.7190472 gauss-seidel spectral radius is 0.9993007 estimated iterations to convergence 298 setup time was (sec) 1.350000 now iterating at: 12:01:42 rms-change max change #iterations 10.00024 446.3793 at 10iterations 5.927215 146.3226 at 20iterations 3.507844 77.34311 at 30iterations 2.069311 46.12598 at 40iterations 1.215956 23.87348 at 50iterations 0.7127136 14.09560 at 60iterations 0.4173730 8.988827 at 70iterations 0.2452732 4.810782 at 80iterations 0.1434756 2.639093 at 90iterations 8.3915763E-02 1.485923 at 100iterations 4.9059059E-02 1.000546 at 110iterations 2.8631292E-02 0.5209923 at 120iterations 1.6737452E-02 0.3009186 at 130iterations 9.8114545E-03 0.2033615 at 140iterations 5.7446500E-03 0.1167622 at 150iterations 3.3641839E-03 6.5677643E-02 at 160iterations 1.9728935E-03 3.6612868E-02 at 170iterations 1.1631346E-03 2.3370743E-02 at 180iterations finished qdiffx linear iterations at : 12:01:54 total time elapsed so far: 12.96000 # loops : 180 mean,max change (kT/e) : 1.1631346E-03 2.3370743E-02 energy calculations done at 12.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.10000 DelPhi exited at 12:01:55 13.099u 0.233s 0:13.74 96.9% 0+0k 0+0io 0pf+0w