Sun Oct 9 21:22:58 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 Sun Oct 9 2011 at 21:22:58 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 = 2983 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6337452 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): -9.059999 44.21900 ymin,ymax (A): -27.57800 28.59600 zmin,zma (A): -2.387000 51.92500 x,y,z range (A): 53.27900 56.17400 54.31200 scale (grids/A): 0.6337452 object centre (A): 17.57950 0.5089998 24.76900 number of atom coordinates read : 2983 total number of charged atoms : 2835 net assigned charge : 7.000021 assigned positive charge : 453.2570 centred at (gu) : 91.17419 91.02792 90.13271 assigned negative charge : -446.2582 centred at (gu) : 91.17904 90.92206 90.09317 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7944 nv = 96 ne = 84 npr = 58868 no. pairs analyzed = 58868 no. exposed pairs = 3909 no. arc points = 28238 no. surface atoms = 1308 nbur = 1675 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 429 mr = 4022 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.2100000 number of dielectric boundary points 4297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2842 ## 299 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9709 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7764498E-09 1.3152156E-08 midg,1,midg; midg,igrid,midg -2.8879239E-09 2.5164834E-08 1,midg,midg; igrid,midg,midg 6.9723041E-09 9.9723332E-09 gauss-seidel spectral radius is 0.9871458 estimated iterations to convergence 72 setup time was (sec) 0.3900000 now iterating at: 21:22:59 rms-change max change #iterations 0.1457233 19.28496 at 10iterations 1.4106371E-02 1.877426 at 20iterations 1.3781168E-03 0.2007599 at 30iterations 1.3543868E-04 1.9418716E-02 at 40iterations 1.4239184E-05 1.9302368E-03 at 50iterations finished qdiffx linear iterations at : 21:23:01 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.4239184E-05 1.9302368E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 21:23:02 3.346u 0.185s 0:03.82 92.1% 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 21:23:02 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 = 2983 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.901236 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): -9.059999 44.21900 ymin,ymax (A): -27.57800 28.59600 zmin,zma (A): -2.387000 51.92500 x,y,z range (A): 53.27900 56.17400 54.31200 scale (grids/A): 1.901236 object centre (A): 17.57950 0.5089998 24.76900 number of atom coordinates read : 2983 total number of charged atoms : 2835 net assigned charge : 7.000021 assigned positive charge : 453.2570 centred at (gu) : 93.52200 93.08333 90.39734 assigned negative charge : -446.2582 centred at (gu) : 93.53665 92.76581 90.27901 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 85384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28238 grid for indexing accessible points = 1.400000 m= 28933 mr = 56124 m= 4476 mr = 20444 m= 273 mr = 2669 m= 2 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1911 time to turn everything in is 0.4200000 number of dielectric boundary points 39709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 188 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 22261 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) : 0.6337452 object centre at (A) : 17.57950 0.5089998 24.76900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8497797E-02 1.9076732E-03 midg,1,midg; midg,igrid,midg 1.6599195E-02 1.8131630E-02 1,midg,midg; igrid,midg,midg 2.9228569E-03 -6.4589223E-03 gauss-seidel spectral radius is 0.9986829 estimated iterations to convergence 218 setup time was (sec) 0.6300000 now iterating at: 21:23:03 rms-change max change #iterations 4.526492 167.1403 at 10iterations 2.138372 75.64352 at 20iterations 1.011008 37.39508 at 30iterations 0.4774417 14.86079 at 40iterations 0.2263016 6.669744 at 50iterations 0.1070978 3.376411 at 60iterations 5.0610915E-02 1.868622 at 70iterations 2.4023946E-02 0.7185776 at 80iterations 1.1392875E-02 0.3473988 at 90iterations 5.4112715E-03 0.1647072 at 100iterations 2.5504315E-03 7.6087952E-02 at 110iterations 1.2120332E-03 3.5905838E-02 at 120iterations finished qdiffx linear iterations at : 21:23:10 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 1.2120332E-03 3.5905838E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 21:23:10 7.799u 0.183s 0:08.26 96.4% 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 Sun Oct 9 2011 at 21:23:10 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 = 2983 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.851853 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): -9.059999 44.21900 ymin,ymax (A): -27.57800 28.59600 zmin,zma (A): -2.387000 51.92500 x,y,z range (A): 53.27900 56.17400 54.31200 scale (grids/A): 2.851853 object centre (A): 17.57950 0.5089998 24.76900 number of atom coordinates read : 2983 total number of charged atoms : 2835 net assigned charge : 7.000021 assigned positive charge : 453.2570 centred at (gu) : 95.28282 94.62465 90.59593 assigned negative charge : -446.2582 centred at (gu) : 95.30486 94.14871 90.41856 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 197485 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28238 grid for indexing accessible points = 1.400000 m= 93799 mr = 136791 m= 32669 mr = 74671 m= 7860 mr = 25373 m= 1238 mr = 5747 m= 77 mr = 868 m= 2 mr = 55 m= 0 mr = 2 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 6986 time to turn everything in is 1.050000 number of dielectric boundary points 89623 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 22679 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) : 1.901236 object centre at (A) : 17.57950 0.5089998 24.76900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2285180 -0.1234538 midg,1,midg; midg,igrid,midg 0.1451845 0.1657792 1,midg,midg; igrid,midg,midg 0.1015074 -0.2910872 gauss-seidel spectral radius is 0.9992905 estimated iterations to convergence 296 setup time was (sec) 1.300000 now iterating at: 21:23:12 rms-change max change #iterations 10.83626 312.7527 at 10iterations 6.448338 140.1560 at 20iterations 3.823153 79.85616 at 30iterations 2.256870 46.76270 at 40iterations 1.322598 26.00884 at 50iterations 0.7752433 13.86419 at 60iterations 0.4531511 7.716526 at 70iterations 0.2644851 5.748737 at 80iterations 0.1543943 2.738726 at 90iterations 8.9830592E-02 1.600357 at 100iterations 5.2360516E-02 0.9752980 at 110iterations 3.0445639E-02 0.5715691 at 120iterations 1.7684622E-02 0.2948177 at 130iterations 1.0288227E-02 0.1829796 at 140iterations 5.9860717E-03 9.9117279E-02 at 150iterations 3.4739887E-03 5.8532715E-02 at 160iterations 2.0215246E-03 3.3355713E-02 at 170iterations 1.1768340E-03 1.9540668E-02 at 180iterations finished qdiffx linear iterations at : 21:23:23 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 1.1768340E-03 1.9540668E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 21:23:24 12.872u 0.210s 0:13.34 98.0% 0+0k 0+0io 0pf+0w