Sun Oct 9 08:15:14 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 08:15:14 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3271 !!! WARNING: GLM 153 has a net charge of -0.0940 !!! WARNING: NDP 531 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5780159 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): 44.82000 106.4100 ymin,ymax (A): 20.46500 77.23300 zmin,zma (A): 10.69800 60.97700 x,y,z range (A): 61.59000 56.76800 50.27900 scale (grids/A): 0.5780159 object centre (A): 75.61501 48.84900 35.83750 number of atom coordinates read : 3271 total number of charged atoms : 3127 net assigned charge : 4.906013 assigned positive charge : 489.5239 centred at (gu) : 90.63248 90.68523 88.67310 assigned negative charge : -484.6189 centred at (gu) : 90.79826 90.63703 88.71035 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7159 nv = 96 ne = 84 npr = 66938 no. pairs analyzed = 66938 no. exposed pairs = 3919 no. arc points = 27612 no. surface atoms = 1313 nbur = 1958 mkacc time = 0.1100000 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 = 1.512000 m= 315 mr = 3916 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2793 ## 296 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9222 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5097007E-09 1.3430379E-10 midg,1,midg; midg,igrid,midg -6.0428877E-11 2.4435740E-09 1,midg,midg; igrid,midg,midg 4.0055959E-09 -3.2481422E-09 gauss-seidel spectral radius is 0.9845755 estimated iterations to convergence 66 setup time was (sec) 0.4400000 now iterating at: 08:15:14 rms-change max change #iterations 0.1063718 15.10519 at 10iterations 8.2755769E-03 1.408546 at 20iterations 6.5765862E-04 8.8603973E-02 at 30iterations 6.5554588E-05 1.0125160E-02 at 40iterations 1.0099088E-05 1.2921095E-03 at 50iterations finished qdiffx linear iterations at : 08:15:17 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.0099088E-05 1.2921095E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 08:15:18 3.438u 0.180s 0:04.10 88.0% 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 08:15:18 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3271 !!! WARNING: GLM 153 has a net charge of -0.0940 !!! WARNING: NDP 531 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.734048 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): 44.82000 106.4100 ymin,ymax (A): 20.46500 77.23300 zmin,zma (A): 10.69800 60.97700 x,y,z range (A): 61.59000 56.76800 50.27900 scale (grids/A): 1.734048 object centre (A): 75.61501 48.84900 35.83750 number of atom coordinates read : 3271 total number of charged atoms : 3127 net assigned charge : 4.906013 assigned positive charge : 489.5239 centred at (gu) : 91.89668 92.05450 86.01831 assigned negative charge : -484.6189 centred at (gu) : 92.39430 91.91062 86.13068 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 78861 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27612 grid for indexing accessible points = 1.400000 m= 26723 mr = 55081 m= 3171 mr = 19182 m= 114 mr = 1713 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 756 time to turn everything in is 0.3900000 number of dielectric boundary points 32875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 237 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 24293 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) : 0.5780159 object centre at (A) : 75.61501 48.84900 35.83750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2764669E-03 -2.2204658E-03 midg,1,midg; midg,igrid,midg -1.0148264E-02 4.6072025E-03 1,midg,midg; igrid,midg,midg 4.4324744E-02 -1.5018545E-02 gauss-seidel spectral radius is 0.9984271 estimated iterations to convergence 200 setup time was (sec) 0.6300000 now iterating at: 08:15:19 rms-change max change #iterations 4.000646 154.5988 at 10iterations 1.766533 60.21046 at 20iterations 0.7827527 25.23068 at 30iterations 0.3470761 11.10458 at 40iterations 0.1535433 4.673637 at 50iterations 6.8257570E-02 2.418406 at 60iterations 3.0241361E-02 0.9731069 at 70iterations 1.3493626E-02 0.4090710 at 80iterations 5.9591965E-03 0.1888742 at 90iterations 2.6390580E-03 8.7333679E-02 at 100iterations 1.1769595E-03 3.9670944E-02 at 110iterations 5.2141718E-04 1.6725540E-02 at 120iterations finished qdiffx linear iterations at : 08:15:27 total time elapsed so far: 8.440000 # loops : 120 mean,max change (kT/e) : 5.2141718E-04 1.6725540E-02 energy calculations done at 8.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.600000 DelPhi exited at 08:15:27 8.605u 0.231s 0:09.27 95.2% 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 08:15:27 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3271 !!! WARNING: GLM 153 has a net charge of -0.0940 !!! WARNING: NDP 531 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.601071 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): 44.82000 106.4100 ymin,ymax (A): 20.46500 77.23300 zmin,zma (A): 10.69800 60.97700 x,y,z range (A): 61.59000 56.76800 50.27900 scale (grids/A): 2.601071 object centre (A): 75.61501 48.84900 35.83750 number of atom coordinates read : 3271 total number of charged atoms : 3127 net assigned charge : 4.906013 assigned positive charge : 489.5239 centred at (gu) : 92.84495 93.08153 84.02738 assigned negative charge : -484.6189 centred at (gu) : 93.59117 92.86580 84.19591 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 183352 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27612 grid for indexing accessible points = 1.400000 m= 88935 mr = 134417 m= 28967 mr = 71901 m= 5323 mr = 22770 m= 514 mr = 3637 m= 7 mr = 282 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 2385 time to turn everything in is 1.040000 number of dielectric boundary points 74091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 25004 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) : 1.734048 object centre at (A) : 75.61501 48.84900 35.83750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9336880E-02 -3.8689014E-02 midg,1,midg; midg,igrid,midg -0.1953311 5.0217442E-02 1,midg,midg; igrid,midg,midg 0.4938790 -0.1988020 gauss-seidel spectral radius is 0.9992152 estimated iterations to convergence 282 setup time was (sec) 1.310000 now iterating at: 08:15:29 rms-change max change #iterations 9.941598 313.3200 at 10iterations 5.762741 137.4275 at 20iterations 3.317247 73.62686 at 30iterations 1.899418 43.80424 at 40iterations 1.086757 22.60789 at 50iterations 0.6193759 11.94125 at 60iterations 0.3522054 7.602989 at 70iterations 0.2001693 4.212086 at 80iterations 0.1136572 2.436427 at 90iterations 6.4488575E-02 1.317179 at 100iterations 3.6501341E-02 0.6312559 at 110iterations 2.0677373E-02 0.4125614 at 120iterations 1.1717965E-02 0.2119187 at 130iterations 6.6357777E-03 0.1326332 at 140iterations 3.7479994E-03 6.8203926E-02 at 150iterations 2.1225484E-03 3.8909912E-02 at 160iterations 1.2017426E-03 2.2056580E-02 at 170iterations 6.7883357E-04 1.2275696E-02 at 180iterations finished qdiffx linear iterations at : 08:15:41 total time elapsed so far: 13.87000 # loops : 180 mean,max change (kT/e) : 6.7883357E-04 1.2275696E-02 energy calculations done at 13.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.99000 DelPhi exited at 08:15:42 13.996u 0.209s 0:14.69 96.5% 0+0k 0+0io 0pf+0w