Mon Oct 10 17:01:35 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 Mon Oct 10 2011 at 17:01:35 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2838 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: 0.5785607 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): -10.93900 39.59600 ymin,ymax (A): -24.06100 29.77500 zmin,zma (A): 13.82200 75.35400 x,y,z range (A): 50.53500 53.83600 61.53201 scale (grids/A): 0.5785607 object centre (A): 14.32850 2.857000 44.58800 number of atom coordinates read : 2838 total number of charged atoms : 2697 net assigned charge : 1.000026 assigned positive charge : 420.4525 centred at (gu) : 89.75542 89.21931 89.86123 assigned negative charge : -419.4534 centred at (gu) : 89.72110 89.36465 89.96783 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6329 nv = 96 ne = 84 npr = 57198 no. pairs analyzed = 57198 no. exposed pairs = 3528 no. arc points = 25662 no. surface atoms = 1191 nbur = 1647 mkacc time = 8.9999996E-02 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 = 1.484000 m= 290 mr = 3324 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2650 ## 296 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8097 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3461109E-09 -1.8903075E-09 midg,1,midg; midg,igrid,midg 3.6334991E-09 -2.2780575E-09 1,midg,midg; igrid,midg,midg -5.2861676E-10 8.1342988E-10 gauss-seidel spectral radius is 0.9845743 estimated iterations to convergence 66 setup time was (sec) 0.4100000 now iterating at: 17:01:36 rms-change max change #iterations 9.3031794E-02 17.83843 at 10iterations 7.2772810E-03 1.186068 at 20iterations 5.6011928E-04 8.0528259E-02 at 30iterations 4.3126412E-05 6.0424805E-03 at 40iterations 3.3621698E-06 5.9032440E-04 at 50iterations finished qdiffx linear iterations at : 17:01:39 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 3.3621698E-06 5.9032440E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 17:01:40 3.421u 0.157s 0:04.55 78.4% 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 17:01:40 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 = 2838 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.735682 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): -10.93900 39.59600 ymin,ymax (A): -24.06100 29.77500 zmin,zma (A): 13.82200 75.35400 x,y,z range (A): 50.53500 53.83600 61.53201 scale (grids/A): 1.735682 object centre (A): 14.32850 2.857000 44.58800 number of atom coordinates read : 2838 total number of charged atoms : 2697 net assigned charge : 1.000026 assigned positive charge : 420.4525 centred at (gu) : 89.26517 87.65717 89.58285 assigned negative charge : -419.4534 centred at (gu) : 89.16290 88.09341 89.90324 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69742 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25662 grid for indexing accessible points = 1.400000 m= 22493 mr = 47429 m= 2676 mr = 15793 m= 89 mr = 1464 m= 0 mr = 14 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1461 time to turn everything in is 0.3300000 number of dielectric boundary points 30300 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 259 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 20988 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) : 0.5785607 object centre at (A) : 14.32850 2.857000 44.58800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6099369E-02 -5.0781500E-03 midg,1,midg; midg,igrid,midg 8.7539786E-03 -1.8331520E-02 1,midg,midg; igrid,midg,midg -1.3271596E-03 -3.7134853E-03 gauss-seidel spectral radius is 0.9983909 estimated iterations to convergence 198 setup time was (sec) 0.5600000 now iterating at: 17:01:40 rms-change max change #iterations 3.712121 169.5705 at 10iterations 1.621958 59.34058 at 20iterations 0.7088515 25.11108 at 30iterations 0.3128971 9.880052 at 40iterations 0.1361454 4.894432 at 50iterations 6.0107972E-02 2.155855 at 60iterations 2.6262751E-02 0.8379612 at 70iterations 1.1551907E-02 0.4388990 at 80iterations 5.0658570E-03 0.1810748 at 90iterations 2.2266735E-03 7.2740555E-02 at 100iterations 9.7539410E-04 3.0472755E-02 at 110iterations 4.3047778E-04 1.4923751E-02 at 120iterations finished qdiffx linear iterations at : 17:01:47 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 4.3047778E-04 1.4923751E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 17:01:48 7.754u 0.183s 0:08.42 94.1% 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 Mon Oct 10 2011 at 17:01:48 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 = 2838 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: 2.603523 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): -10.93900 39.59600 ymin,ymax (A): -24.06100 29.77500 zmin,zma (A): 13.82200 75.35400 x,y,z range (A): 50.53500 53.83600 61.53201 scale (grids/A): 2.603523 object centre (A): 14.32850 2.857000 44.58800 number of atom coordinates read : 2838 total number of charged atoms : 2697 net assigned charge : 1.000026 assigned positive charge : 420.4525 centred at (gu) : 88.89767 86.48556 89.37402 assigned negative charge : -419.4534 centred at (gu) : 88.74423 87.14007 89.85487 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 161691 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25662 grid for indexing accessible points = 1.400000 m= 76232 mr = 115634 m= 23559 mr = 60983 m= 4566 mr = 18131 m= 381 mr = 3164 m= 7 mr = 209 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 4965 time to turn everything in is 0.8300000 number of dielectric boundary points 68315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 21570 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) : 1.735682 object centre at (A) : 14.32850 2.857000 44.58800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3058366 -6.5776952E-02 midg,1,midg; midg,igrid,midg 9.2880271E-02 -0.2211833 1,midg,midg; igrid,midg,midg -4.5642447E-02 -5.6922656E-02 gauss-seidel spectral radius is 0.9992000 estimated iterations to convergence 279 setup time was (sec) 1.070000 now iterating at: 17:01:49 rms-change max change #iterations 9.073666 291.7703 at 10iterations 5.168705 135.8438 at 20iterations 2.926759 92.27994 at 30iterations 1.648437 43.85776 at 40iterations 0.9303187 19.12581 at 50iterations 0.5235403 11.32688 at 60iterations 0.2940906 6.331245 at 70iterations 0.1652977 3.538113 at 80iterations 9.3033053E-02 1.826774 at 90iterations 5.2092623E-02 1.056679 at 100iterations 2.9259222E-02 0.5757828 at 110iterations 1.6454961E-02 0.3366890 at 120iterations 9.2128646E-03 0.1878452 at 130iterations 5.1841582E-03 0.1119347 at 140iterations 2.9047462E-03 5.9677124E-02 at 150iterations 1.6319563E-03 3.1156540E-02 at 160iterations 9.1471901E-04 1.7959595E-02 at 170iterations 5.1357428E-04 9.2873573E-03 at 180iterations finished qdiffx linear iterations at : 17:02:02 total time elapsed so far: 13.36000 # loops : 180 mean,max change (kT/e) : 5.1357428E-04 9.2873573E-03 energy calculations done at 13.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.50000 DelPhi exited at 17:02:03 13.499u 0.229s 0:14.59 93.9% 0+0k 0+0io 0pf+0w