Mon Oct 10 12:27:00 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 12:27:00 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2118 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: 0.7398787 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): -22.82600 24.58600 ymin,ymax (A): -7.856000 36.89800 zmin,zma (A): -3.460000 44.65600 x,y,z range (A): 47.41200 44.75400 48.11600 scale (grids/A): 0.7398787 object centre (A): 0.8800001 14.52100 20.59800 number of atom coordinates read : 2118 total number of charged atoms : 1980 net assigned charge : -3.999990 assigned positive charge : 317.5039 centred at (gu) : 89.45243 90.31415 89.82852 assigned negative charge : -321.5040 centred at (gu) : 89.50237 90.32369 89.96272 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8031 nv = 96 ne = 84 npr = 43511 no. pairs analyzed = 43511 no. exposed pairs = 2705 no. arc points = 18920 no. surface atoms = 918 nbur = 1200 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 540 mr = 4468 m= 5 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.2700000 number of dielectric boundary points 3996 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1518 ## 110 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8410 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6450717E-08 -2.0252645E-07 midg,1,midg; midg,igrid,midg -5.7712651E-08 -8.5203119E-08 1,midg,midg; igrid,midg,midg -2.1874822E-08 -1.1011643E-07 gauss-seidel spectral radius is 0.9904824 estimated iterations to convergence 83 setup time was (sec) 0.5700000 now iterating at: 12:27:01 rms-change max change #iterations 0.2445978 38.38246 at 10iterations 3.3572234E-02 4.354811 at 20iterations 4.3786848E-03 0.5028000 at 30iterations 6.0237222E-04 7.3310852E-02 at 40iterations 8.0240949E-05 1.1276245E-02 at 50iterations finished qdiffx linear iterations at : 12:27:05 total time elapsed so far: 4.510000 # loops : 50 mean,max change (kT/e) : 8.0240949E-05 1.1276245E-02 energy calculations done at 4.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.680000 DelPhi exited at 12:27:05 4.681u 0.422s 0:05.66 90.1% 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 12:27:06 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2118 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: 2.219636 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): -22.82600 24.58600 ymin,ymax (A): -7.856000 36.89800 zmin,zma (A): -3.460000 44.65600 x,y,z range (A): 47.41200 44.75400 48.11600 scale (grids/A): 2.219636 object centre (A): 0.8800001 14.52100 20.59800 number of atom coordinates read : 2118 total number of charged atoms : 1980 net assigned charge : -3.999990 assigned positive charge : 317.5039 centred at (gu) : 88.35735 90.94247 89.48560 assigned negative charge : -321.5040 centred at (gu) : 88.50709 90.97104 89.88815 start vw surface at 0.1000000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 84112 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18920 grid for indexing accessible points = 1.400000 m= 33381 mr = 58137 m= 7161 mr = 25360 m= 727 mr = 4970 m= 25 mr = 402 m= 0 mr = 6 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1303 time to turn everything in is 0.7100000 number of dielectric boundary points 36531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 38 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 15763 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) : 0.7398787 object centre at (A) : 0.8800001 14.52100 20.59800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6185059E-03 -0.1089189 midg,1,midg; midg,igrid,midg -2.7715422E-02 -2.3060216E-02 1,midg,midg; igrid,midg,midg 9.3727633E-03 1.2698531E-02 gauss-seidel spectral radius is 0.9989277 estimated iterations to convergence 242 setup time was (sec) 1.070000 now iterating at: 12:27:07 rms-change max change #iterations 5.099763 233.9503 at 10iterations 2.592035 76.08848 at 20iterations 1.321026 38.84529 at 30iterations 0.6731581 19.96078 at 40iterations 0.3433445 10.37157 at 50iterations 0.1750100 4.814801 at 60iterations 8.9389160E-02 2.396729 at 70iterations 4.5501739E-02 1.295830 at 80iterations 2.3276631E-02 0.6878037 at 90iterations 1.1827209E-02 0.3348980 at 100iterations 6.0522365E-03 0.1965182 at 110iterations 3.0866449E-03 7.9376221E-02 at 120iterations finished qdiffx linear iterations at : 12:27:18 total time elapsed so far: 11.92000 # loops : 120 mean,max change (kT/e) : 3.0866449E-03 7.9376221E-02 energy calculations done at 11.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.09000 DelPhi exited at 12:27:19 12.091u 0.470s 0:12.97 96.8% 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 12:27:19 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2118 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: 3.329454 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): -22.82600 24.58600 ymin,ymax (A): -7.856000 36.89800 zmin,zma (A): -3.460000 44.65600 x,y,z range (A): 47.41200 44.75400 48.11600 scale (grids/A): 3.329454 object centre (A): 0.8800001 14.52100 20.59800 number of atom coordinates read : 2118 total number of charged atoms : 1980 net assigned charge : -3.999990 assigned positive charge : 317.5039 centred at (gu) : 87.53601 91.41357 89.22836 assigned negative charge : -321.5040 centred at (gu) : 87.76064 91.45650 89.83226 start vw surface at 0.1100000 fill in re-entrant regions at 0.8800000 boundary points on vw surface= 193732 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18920 grid for indexing accessible points = 1.400000 m= 102417 mr = 139945 m= 43702 mr = 84751 m= 13652 mr = 36313 m= 3051 mr = 10943 m= 426 mr = 2383 m= 30 mr = 264 m= 0 mr = 15 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 4134 time to turn everything in is 2.190000 number of dielectric boundary points 82396 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.330000 number of grid points assigned charge 15840 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) : 2.219636 object centre at (A) : 0.8800001 14.52100 20.59800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0290040E-02 -1.218907 midg,1,midg; midg,igrid,midg -0.2624713 -0.1236873 1,midg,midg; igrid,midg,midg 3.1581473E-02 4.3288346E-02 gauss-seidel spectral radius is 0.9993191 estimated iterations to convergence 302 setup time was (sec) 2.560000 now iterating at: 12:27:22 rms-change max change #iterations 10.98088 311.8310 at 10iterations 6.454774 145.2495 at 20iterations 3.804897 72.67319 at 30iterations 2.234366 35.60792 at 40iterations 1.318742 20.68687 at 50iterations 0.7736599 12.93664 at 60iterations 0.4555772 7.781550 at 70iterations 0.2684831 4.165379 at 80iterations 0.1571231 2.518895 at 90iterations 9.2339657E-02 1.646350 at 100iterations 5.4278094E-02 0.8373718 at 110iterations 3.1817973E-02 0.5665092 at 120iterations 1.8675590E-02 0.3029079 at 130iterations 1.0986771E-02 0.1749268 at 140iterations 6.4560599E-03 0.1174352 at 150iterations 3.7969537E-03 6.3165069E-02 at 160iterations 2.2257320E-03 3.4713745E-02 at 170iterations 1.3071619E-03 2.0612001E-02 at 180iterations finished qdiffx linear iterations at : 12:27:39 total time elapsed so far: 19.99000 # loops : 180 mean,max change (kT/e) : 1.3071619E-03 2.0612001E-02 energy calculations done at 19.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.15000 DelPhi exited at 12:27:40 20.158u 0.493s 0:21.00 98.2% 0+0k 0+0io 0pf+0w