Mon Oct 10 10:29:30 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 10:29:30 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2825 !!! WARNING: HIT 235 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5464649 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): -22.32600 42.82000 ymin,ymax (A): -12.63300 45.35800 zmin,zma (A): -2.190000 50.84400 x,y,z range (A): 65.14600 57.99100 53.03400 scale (grids/A): 0.5464649 object centre (A): 10.24700 16.36250 24.32700 number of atom coordinates read : 2825 total number of charged atoms : 2675 net assigned charge : 8.014026 assigned positive charge : 414.0539 centred at (gu) : 91.66306 91.27498 86.98688 assigned negative charge : -406.0403 centred at (gu) : 91.74144 91.32362 86.80019 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5647 nv = 96 ne = 84 npr = 55044 no. pairs analyzed = 55044 no. exposed pairs = 4299 no. arc points = 30851 no. surface atoms = 1424 nbur = 1401 mkacc time = 0.1300000 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 = 1.568000 m= 254 mr = 2434 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3006 ## 378 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7284 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3508336E-09 7.9624057E-10 midg,1,midg; midg,igrid,midg 6.2058736E-10 3.4355713E-10 1,midg,midg; igrid,midg,midg 6.8256079E-10 9.6536258E-11 gauss-seidel spectral radius is 0.9827397 estimated iterations to convergence 63 setup time was (sec) 0.5900000 now iterating at: 10:29:31 rms-change max change #iterations 7.1088940E-02 13.43320 at 10iterations 4.7344691E-03 0.8816185 at 20iterations 3.2668648E-04 5.7596207E-02 at 30iterations 3.0596584E-05 4.0340424E-03 at 40iterations 4.9788719E-06 5.8984756E-04 at 50iterations finished qdiffx linear iterations at : 10:29:34 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 4.9788719E-06 5.8984756E-04 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 10:29:34 3.535u 0.160s 0:03.99 92.4% 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 10:29:34 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2825 !!! WARNING: HIT 235 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.639395 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): -22.32600 42.82000 ymin,ymax (A): -12.63300 45.35800 zmin,zma (A): -2.190000 50.84400 x,y,z range (A): 65.14600 57.99100 53.03400 scale (grids/A): 1.639395 object centre (A): 10.24700 16.36250 24.32700 number of atom coordinates read : 2825 total number of charged atoms : 2675 net assigned charge : 8.014026 assigned positive charge : 414.0539 centred at (gu) : 94.98879 93.82456 80.96018 assigned negative charge : -406.0403 centred at (gu) : 95.22388 93.97057 80.40038 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 60736 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30851 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 17821 mr = 36637 m= 1859 mr = 10910 m= 49 mr = 657 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 225 time to turn everything in is 0.5000000 number of dielectric boundary points 32261 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 310 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 20508 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) : 0.5464649 object centre at (A) : 10.24700 16.36250 24.32700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5048221E-03 7.8959269E-03 midg,1,midg; midg,igrid,midg 1.4572891E-02 1.3971073E-02 1,midg,midg; igrid,midg,midg -1.2099002E-02 -1.4530784E-02 gauss-seidel spectral radius is 0.9981965 estimated iterations to convergence 187 setup time was (sec) 0.8100000 now iterating at: 10:29:35 rms-change max change #iterations 3.190575 180.7206 at 10iterations 1.323592 61.11399 at 20iterations 0.5477793 21.52879 at 30iterations 0.2275395 8.737865 at 40iterations 9.5001385E-02 3.815819 at 50iterations 3.9582070E-02 1.451730 at 60iterations 1.6528573E-02 0.7246952 at 70iterations 6.8931873E-03 0.2540627 at 80iterations 2.8688186E-03 0.1322808 at 90iterations 1.1946160E-03 4.3186188E-02 at 100iterations 4.9907400E-04 1.8585205E-02 at 110iterations 2.0961316E-04 8.6746216E-03 at 120iterations finished qdiffx linear iterations at : 10:29:42 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 2.0961316E-04 8.6746216E-03 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.050000 DelPhi exited at 10:29:43 8.056u 0.248s 0:08.57 96.7% 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 10:29:43 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2825 !!! WARNING: HIT 235 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.459092 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): -22.32600 42.82000 ymin,ymax (A): -12.63300 45.35800 zmin,zma (A): -2.190000 50.84400 x,y,z range (A): 65.14600 57.99100 53.03400 scale (grids/A): 2.459092 object centre (A): 10.24700 16.36250 24.32700 number of atom coordinates read : 2825 total number of charged atoms : 2675 net assigned charge : 8.014026 assigned positive charge : 414.0539 centred at (gu) : 97.48291 95.73692 76.44008 assigned negative charge : -406.0403 centred at (gu) : 97.83581 95.95573 75.60050 start vw surface at 0.1700000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 140708 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30851 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 60780 mr = 91088 m= 17369 mr = 44523 m= 2708 mr = 11803 m= 174 mr = 1358 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 769 time to turn everything in is 1.200000 number of dielectric boundary points 72922 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 21377 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) : 1.639395 object centre at (A) : 10.24700 16.36250 24.32700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5720695E-02 9.2941761E-02 midg,1,midg; midg,igrid,midg 0.3200457 0.1975412 1,midg,midg; igrid,midg,midg -0.5463926 -0.4914518 gauss-seidel spectral radius is 0.9991453 estimated iterations to convergence 270 setup time was (sec) 1.530000 now iterating at: 10:29:45 rms-change max change #iterations 8.543879 270.9569 at 10iterations 4.912613 136.5819 at 20iterations 2.793461 76.14828 at 30iterations 1.571056 44.85817 at 40iterations 0.8783392 23.78162 at 50iterations 0.4898126 13.43324 at 60iterations 0.2729888 6.438478 at 70iterations 0.1512504 3.866650 at 80iterations 8.3843902E-02 2.224208 at 90iterations 4.6537105E-02 1.127470 at 100iterations 2.5641384E-02 0.6185551 at 110iterations 1.4142553E-02 0.3304243 at 120iterations 7.8297434E-03 0.1682138 at 130iterations 4.3247570E-03 0.1056290 at 140iterations 2.3822200E-03 5.5164337E-02 at 150iterations 1.3137718E-03 3.0285358E-02 at 160iterations 7.2332198E-04 1.7909050E-02 at 170iterations 3.9935179E-04 1.0246277E-02 at 180iterations finished qdiffx linear iterations at : 10:29:55 total time elapsed so far: 12.22000 # loops : 180 mean,max change (kT/e) : 3.9935179E-04 1.0246277E-02 energy calculations done at 12.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.43000 DelPhi exited at 10:29:56 12.432u 0.210s 0:12.93 97.7% 0+0k 0+0io 0pf+0w