Sun Oct 9 13:18:12 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 13:18:12 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2385 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: 0.6925800 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): -4.903000 43.93300 ymin,ymax (A): -14.35400 37.04800 zmin,zma (A): 2.235000 44.98100 x,y,z range (A): 48.83600 51.40200 42.74600 scale (grids/A): 0.6925800 object centre (A): 19.51500 11.34700 23.60800 number of atom coordinates read : 2385 total number of charged atoms : 2243 net assigned charge : 2.500021 assigned positive charge : 366.6771 centred at (gu) : 89.09345 90.98743 90.51582 assigned negative charge : -364.1774 centred at (gu) : 89.09615 91.18696 90.56986 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7690 nv = 96 ne = 84 npr = 48549 no. pairs analyzed = 48549 no. exposed pairs = 3013 no. arc points = 21139 no. surface atoms = 1001 nbur = 1384 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 441 mr = 4233 m= 2 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2016 ## 183 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8780 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4207876E-08 -7.2903661E-09 midg,1,midg; midg,igrid,midg 7.8845133E-08 -8.3171301E-08 1,midg,midg; igrid,midg,midg 2.0202751E-08 1.2386843E-08 gauss-seidel spectral radius is 0.9891683 estimated iterations to convergence 78 setup time was (sec) 0.3700000 now iterating at: 13:18:13 rms-change max change #iterations 0.1984016 29.70423 at 10iterations 2.4217442E-02 3.324024 at 20iterations 3.2728894E-03 0.4300156 at 30iterations 6.3135911E-04 9.2056274E-02 at 40iterations 1.7942514E-04 2.7950287E-02 at 50iterations finished qdiffx linear iterations at : 13:18:16 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.7942514E-04 2.7950287E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 13:18:16 3.350u 0.168s 0:03.78 92.8% 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 Sun Oct 9 2011 at 13:18:16 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2385 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: 2.077740 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): -4.903000 43.93300 ymin,ymax (A): -14.35400 37.04800 zmin,zma (A): 2.235000 44.98100 x,y,z range (A): 48.83600 51.40200 42.74600 scale (grids/A): 2.077740 object centre (A): 19.51500 11.34700 23.60800 number of atom coordinates read : 2385 total number of charged atoms : 2243 net assigned charge : 2.500021 assigned positive charge : 366.6771 centred at (gu) : 87.27994 92.96162 91.54697 assigned negative charge : -364.1774 centred at (gu) : 87.28807 93.56058 91.70912 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 82067 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21139 grid for indexing accessible points = 1.400000 m= 31143 mr = 57045 m= 5409 mr = 23061 m= 495 mr = 3439 m= 10 mr = 239 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 35340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 17807 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) : 0.6925800 object centre at (A) : 19.51500 11.34700 23.60800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6526421E-02 1.3906702E-02 midg,1,midg; midg,igrid,midg 2.0873947E-02 -7.3726490E-02 1,midg,midg; igrid,midg,midg 4.6964582E-02 -1.1708182E-02 gauss-seidel spectral radius is 0.9988241 estimated iterations to convergence 231 setup time was (sec) 0.6100000 now iterating at: 13:18:17 rms-change max change #iterations 4.928751 184.7047 at 10iterations 2.427330 88.11382 at 20iterations 1.199209 35.50833 at 30iterations 0.5942398 18.83869 at 40iterations 0.2930516 8.564621 at 50iterations 0.1454733 4.526422 at 60iterations 7.2184071E-02 2.192196 at 70iterations 3.5975598E-02 1.031494 at 80iterations 1.7892465E-02 0.5568981 at 90iterations 8.9939367E-03 0.2904663 at 100iterations 4.6208715E-03 0.1364288 at 110iterations 2.4462047E-03 7.3112488E-02 at 120iterations finished qdiffx linear iterations at : 13:18:24 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 2.4462047E-03 7.3112488E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 13:18:24 7.856u 0.198s 0:08.34 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 13:18:24 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2385 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: 3.116610 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): -4.903000 43.93300 ymin,ymax (A): -14.35400 37.04800 zmin,zma (A): 2.235000 44.98100 x,y,z range (A): 48.83600 51.40200 42.74600 scale (grids/A): 3.116610 object centre (A): 19.51500 11.34700 23.60800 number of atom coordinates read : 2385 total number of charged atoms : 2243 net assigned charge : 2.500021 assigned positive charge : 366.6771 centred at (gu) : 85.91979 94.44235 92.32021 assigned negative charge : -364.1774 centred at (gu) : 85.93204 95.34077 92.56371 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 189149 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21139 grid for indexing accessible points = 1.400000 m= 98663 mr = 137709 m= 37873 mr = 80999 m= 10168 mr = 30596 m= 1972 mr = 7657 m= 227 mr = 1367 m= 9 mr = 160 m= 0 mr = 1 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.230000 number of dielectric boundary points 79572 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 17942 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) : 2.077740 object centre at (A) : 19.51500 11.34700 23.60800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4689441 3.5613690E-02 midg,1,midg; midg,igrid,midg 0.4917221 -0.8191025 1,midg,midg; igrid,midg,midg 0.5728575 -0.3345091 gauss-seidel spectral radius is 0.9992976 estimated iterations to convergence 298 setup time was (sec) 1.470000 now iterating at: 13:18:26 rms-change max change #iterations 11.02882 429.3376 at 10iterations 6.512000 133.5703 at 20iterations 3.841926 68.59202 at 30iterations 2.267586 39.14210 at 40iterations 1.334420 27.34914 at 50iterations 0.7847396 13.98666 at 60iterations 0.4605032 8.980240 at 70iterations 0.2696144 4.713003 at 80iterations 0.1580922 2.644503 at 90iterations 9.2777617E-02 1.586643 at 100iterations 5.4573007E-02 0.9916487 at 110iterations 3.2130983E-02 0.5189711 at 120iterations 1.9085823E-02 0.3386993 at 130iterations 1.1543938E-02 0.2685833 at 140iterations 7.1718344E-03 0.1422958 at 150iterations 4.6605449E-03 9.3292236E-02 at 160iterations 3.2159712E-03 6.7428589E-02 at 170iterations 2.3645179E-03 4.9169540E-02 at 180iterations finished qdiffx linear iterations at : 13:18:38 total time elapsed so far: 12.91000 # loops : 180 mean,max change (kT/e) : 2.3645179E-03 4.9169540E-02 energy calculations done at 12.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 13:18:38 13.047u 0.195s 0:13.56 97.5% 0+0k 0+0io 0pf+0w