Sat Oct 8 17:31:22 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 Sat Oct 8 2011 at 17:31:22 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 = 3508 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 0.5235756 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): 0.3010000 44.45700 ymin,ymax (A): -30.40400 26.23300 zmin,zma (A): 1.267000 69.26100 x,y,z range (A): 44.15600 56.63700 67.99400 scale (grids/A): 0.5235756 object centre (A): 22.37900 -2.085500 35.26400 number of atom coordinates read : 3508 total number of charged atoms : 3361 net assigned charge : -5.771982 assigned positive charge : 531.5441 centred at (gu) : 90.28532 91.78452 90.55751 assigned negative charge : -537.3177 centred at (gu) : 90.24393 91.74052 90.55441 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6046 nv = 96 ne = 84 npr = 71812 no. pairs analyzed = 71812 no. exposed pairs = 4305 no. arc points = 29173 no. surface atoms = 1463 nbur = 2045 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 = 1.624000 m= 228 mr = 3211 m= 0 mr = 6 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3057 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2982 ## 451 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 8147 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3684945E-10 -1.5705801E-10 midg,1,midg; midg,igrid,midg -1.8760223E-10 3.4523077E-12 1,midg,midg; igrid,midg,midg -2.6588071E-10 -9.6780570E-12 gauss-seidel spectral radius is 0.9812421 estimated iterations to convergence 60 setup time was (sec) 0.4500000 now iterating at: 17:31:23 rms-change max change #iterations 6.4312175E-02 10.22447 at 10iterations 4.0580831E-03 0.6644740 at 20iterations 3.9613573E-04 7.0158958E-02 at 30iterations 8.2892715E-05 1.6874313E-02 at 40iterations 2.0663514E-05 4.1818619E-03 at 50iterations finished qdiffx linear iterations at : 17:31:26 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 2.0663514E-05 4.1818619E-03 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 17:31:27 3.616u 0.200s 0:04.09 93.1% 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 Sat Oct 8 2011 at 17:31:27 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 = 3508 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 1.570727 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): 0.3010000 44.45700 ymin,ymax (A): -30.40400 26.23300 zmin,zma (A): 1.267000 69.26100 x,y,z range (A): 44.15600 56.63700 67.99400 scale (grids/A): 1.570727 object centre (A): 22.37900 -2.085500 35.26400 number of atom coordinates read : 3508 total number of charged atoms : 3361 net assigned charge : -5.771982 assigned positive charge : 531.5441 centred at (gu) : 90.85490 95.35286 91.67142 assigned negative charge : -537.3177 centred at (gu) : 90.73125 95.22102 91.66309 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 68224 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29173 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20343 mr = 47346 m= 1867 mr = 13813 m= 34 mr = 805 m= 0 mr = 1 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 432 time to turn everything in is 0.3500000 number of dielectric boundary points 28503 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 424 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 25450 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) : 0.5235756 object centre at (A) : 22.37900 -2.085500 35.26400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4074921E-03 1.1875224E-02 midg,1,midg; midg,igrid,midg -8.0420021E-03 -1.1308197E-02 1,midg,midg; igrid,midg,midg -4.6735499E-03 1.2422372E-03 gauss-seidel spectral radius is 0.9980718 estimated iterations to convergence 181 setup time was (sec) 0.6200000 now iterating at: 17:31:27 rms-change max change #iterations 3.353711 157.9395 at 10iterations 1.359568 53.61533 at 20iterations 0.5518814 20.51009 at 30iterations 0.2250426 7.699044 at 40iterations 9.1211297E-02 3.295406 at 50iterations 3.7137311E-02 1.519691 at 60iterations 1.5177106E-02 0.5333252 at 70iterations 6.1868462E-03 0.2276225 at 80iterations 2.5368161E-03 8.7212563E-02 at 90iterations 1.0536492E-03 4.5631409E-02 at 100iterations 4.4490080E-04 1.7177582E-02 at 110iterations 1.9663307E-04 7.2383881E-03 at 120iterations finished qdiffx linear iterations at : 17:31:35 total time elapsed so far: 8.530000 # loops : 120 mean,max change (kT/e) : 1.9663307E-04 7.2383881E-03 energy calculations done at 8.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.660000 DelPhi exited at 17:31:36 8.664u 0.274s 0:09.24 96.6% 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 8 2011 at 17:31:36 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 = 3508 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 2.356090 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): 0.3010000 44.45700 ymin,ymax (A): -30.40400 26.23300 zmin,zma (A): 1.267000 69.26100 x,y,z range (A): 44.15600 56.63700 67.99400 scale (grids/A): 2.356090 object centre (A): 22.37900 -2.085500 35.26400 number of atom coordinates read : 3508 total number of charged atoms : 3361 net assigned charge : -5.771982 assigned positive charge : 531.5441 centred at (gu) : 91.28220 98.02903 92.50693 assigned negative charge : -537.3177 centred at (gu) : 91.09692 97.83148 92.49450 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 159086 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29173 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 72676 mr = 116360 m= 18899 mr = 57293 m= 2696 mr = 13864 m= 147 mr = 1655 m= 2 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 1613 time to turn everything in is 0.8400000 number of dielectric boundary points 64301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 26848 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) : 1.570727 object centre at (A) : 22.37900 -2.085500 35.26400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2063632 0.1164252 midg,1,midg; midg,igrid,midg -0.1105568 -0.1520564 1,midg,midg; igrid,midg,midg -8.2280040E-02 3.3592429E-02 gauss-seidel spectral radius is 0.9991074 estimated iterations to convergence 264 setup time was (sec) 1.090000 now iterating at: 17:31:37 rms-change max change #iterations 8.872459 287.0899 at 10iterations 4.931062 120.6881 at 20iterations 2.726177 58.80449 at 30iterations 1.499536 34.36436 at 40iterations 0.8222761 16.97297 at 50iterations 0.4488857 9.426819 at 60iterations 0.2458722 5.472391 at 70iterations 0.1338363 2.821326 at 80iterations 7.3048972E-02 1.435109 at 90iterations 3.9752517E-02 0.8318243 at 100iterations 2.1656765E-02 0.4182739 at 110iterations 1.1803840E-02 0.2384033 at 120iterations 6.4314990E-03 0.1330318 at 130iterations 3.5078374E-03 6.8061829E-02 at 140iterations 1.9147462E-03 4.4109344E-02 at 150iterations 1.0457659E-03 2.2320271E-02 at 160iterations 5.7563110E-04 1.1747360E-02 at 170iterations 3.1894073E-04 6.7869425E-03 at 180iterations finished qdiffx linear iterations at : 17:31:49 total time elapsed so far: 12.84000 # loops : 180 mean,max change (kT/e) : 3.1894073E-04 6.7869425E-03 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.98000 DelPhi exited at 17:31:49 12.980u 0.245s 0:13.51 97.8% 0+0k 0+0io 0pf+0w