Sun Oct 9 10:38:30 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 Sun Oct 9 2011 at 10:38:30 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2658 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: 0.6392645 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): -3.770000 51.91900 ymin,ymax (A): 3.788000 54.40600 zmin,zma (A): 17.50800 69.04200 x,y,z range (A): 55.68900 50.61800 51.53400 scale (grids/A): 0.6392645 object centre (A): 24.07450 29.09700 43.27500 number of atom coordinates read : 2658 total number of charged atoms : 2516 net assigned charge : -2.499978 assigned positive charge : 380.9105 centred at (gu) : 87.46049 90.26193 90.20340 assigned negative charge : -383.4118 centred at (gu) : 87.37418 90.22182 90.37681 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7596 nv = 96 ne = 84 npr = 53012 no. pairs analyzed = 53012 no. exposed pairs = 3768 no. arc points = 26829 no. surface atoms = 1266 nbur = 1392 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 457 mr = 3787 m= 4 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.3200000 number of dielectric boundary points 4188 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2450 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8824 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5164481E-08 -2.4052088E-08 midg,1,midg; midg,igrid,midg -7.3035853E-09 1.3526997E-09 1,midg,midg; igrid,midg,midg -2.2612447E-08 3.6314136E-09 gauss-seidel spectral radius is 0.9873461 estimated iterations to convergence 73 setup time was (sec) 0.5900000 now iterating at: 10:38:31 rms-change max change #iterations 0.1458529 26.49595 at 10iterations 1.4295199E-02 1.830299 at 20iterations 1.4700230E-03 0.1965122 at 30iterations 1.8920169E-04 3.4538269E-02 at 40iterations 4.2897220E-05 8.2330704E-03 at 50iterations finished qdiffx linear iterations at : 10:38:34 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 4.2897220E-05 8.2330704E-03 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 10:38:35 3.715u 0.236s 0:04.32 91.2% 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 Sun Oct 9 2011 at 10:38:35 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2658 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: 1.917794 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): -3.770000 51.91900 ymin,ymax (A): 3.788000 54.40600 zmin,zma (A): 17.50800 69.04200 x,y,z range (A): 55.68900 50.61800 51.53400 scale (grids/A): 1.917794 object centre (A): 24.07450 29.09700 43.27500 number of atom coordinates read : 2658 total number of charged atoms : 2516 net assigned charge : -2.499978 assigned positive charge : 380.9105 centred at (gu) : 82.38080 90.78497 90.60970 assigned negative charge : -383.4118 centred at (gu) : 82.12256 90.66548 91.13052 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 80321 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26829 grid for indexing accessible points = 1.400000 m= 29753 mr = 52440 m= 5422 mr = 21315 m= 329 mr = 3378 m= 5 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 869 time to turn everything in is 0.6300000 number of dielectric boundary points 38599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 19876 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) : 0.6392645 object centre at (A) : 24.07450 29.09700 43.27500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0506446E-02 -2.3895696E-02 midg,1,midg; midg,igrid,midg -6.7176152E-04 3.1471249E-02 1,midg,midg; igrid,midg,midg -5.0454927E-03 -8.2308482E-03 gauss-seidel spectral radius is 0.9986888 estimated iterations to convergence 219 setup time was (sec) 0.9600000 now iterating at: 10:38:36 rms-change max change #iterations 4.263537 201.1258 at 10iterations 2.013630 68.84313 at 20iterations 0.9556608 29.14513 at 30iterations 0.4551103 14.33961 at 40iterations 0.2152884 6.430080 at 50iterations 0.1027917 3.128117 at 60iterations 4.8844326E-02 1.526531 at 70iterations 2.3187267E-02 0.7367554 at 80iterations 1.0999192E-02 0.3221321 at 90iterations 5.2485010E-03 0.1628611 at 100iterations 2.5031653E-03 7.3317766E-02 at 110iterations 1.1937653E-03 3.6102295E-02 at 120iterations finished qdiffx linear iterations at : 10:38:44 total time elapsed so far: 8.430000 # loops : 120 mean,max change (kT/e) : 1.1937653E-03 3.6102295E-02 energy calculations done at 8.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.630000 DelPhi exited at 10:38:44 8.631u 0.262s 0:09.25 96.1% 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 Sun Oct 9 2011 at 10:38:44 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2658 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: 2.876690 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): -3.770000 51.91900 ymin,ymax (A): 3.788000 54.40600 zmin,zma (A): 17.50800 69.04200 x,y,z range (A): 55.68900 50.61800 51.53400 scale (grids/A): 2.876690 object centre (A): 24.07450 29.09700 43.27500 number of atom coordinates read : 2658 total number of charged atoms : 2516 net assigned charge : -2.499978 assigned positive charge : 380.9105 centred at (gu) : 78.57087 91.17731 90.91424 assigned negative charge : -383.4118 centred at (gu) : 78.18393 90.99817 91.69570 start vw surface at 0.1600000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 185075 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26829 grid for indexing accessible points = 1.400000 m= 93008 mr = 127751 m= 36656 mr = 74019 m= 9966 mr = 29093 m= 1501 mr = 7402 m= 66 mr = 926 m= 0 mr = 13 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 2856 time to turn everything in is 1.630000 number of dielectric boundary points 87068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 20127 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) : 1.917794 object centre at (A) : 24.07450 29.09700 43.27500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2179444 -0.1480615 midg,1,midg; midg,igrid,midg 3.2735184E-02 0.4049045 1,midg,midg; igrid,midg,midg 0.2739152 -0.1798786 gauss-seidel spectral radius is 0.9992981 estimated iterations to convergence 298 setup time was (sec) 1.990000 now iterating at: 10:38:46 rms-change max change #iterations 10.24230 469.8298 at 10iterations 6.122160 135.2868 at 20iterations 3.657725 76.26724 at 30iterations 2.169742 41.91458 at 40iterations 1.283019 22.91764 at 50iterations 0.7543487 15.54152 at 60iterations 0.4433169 7.871859 at 70iterations 0.2608333 4.973918 at 80iterations 0.1526644 2.844940 at 90iterations 8.9360267E-02 1.614509 at 100iterations 5.2454833E-02 1.025278 at 110iterations 3.0601773E-02 0.5234566 at 120iterations 1.7849365E-02 0.3263210 at 130iterations 1.0465720E-02 0.1861706 at 140iterations 6.1053080E-03 0.1115780 at 150iterations 3.5567291E-03 7.3730126E-02 at 160iterations 2.0798582E-03 4.0397644E-02 at 170iterations 1.2139132E-03 2.1808624E-02 at 180iterations finished qdiffx linear iterations at : 10:38:59 total time elapsed so far: 14.58000 # loops : 180 mean,max change (kT/e) : 1.2139132E-03 2.1808624E-02 energy calculations done at 14.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.77000 DelPhi exited at 10:39:00 14.776u 0.279s 0:15.39 97.7% 0+0k 0+0io 0pf+0w