Sat Oct 15 12:39:56 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 Sat Oct 15 2011 at 12:39:56 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 = 5720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5008019 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): 3.820000 74.90600 ymin,ymax (A): 17.62500 84.07500 zmin,zma (A): 6.450000 75.19400 x,y,z range (A): 71.08600 66.45000 68.74400 scale (grids/A): 0.5008019 object centre (A): 39.36300 50.85000 40.82200 number of atom coordinates read : 5720 total number of charged atoms : 5550 net assigned charge : -6.999978 assigned positive charge : 858.9704 centred at (gu) : 89.62936 89.33990 89.27607 assigned negative charge : -865.9777 centred at (gu) : 89.57681 89.33614 89.21986 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8956 nv = 96 ne = 84 npr = 115804 no. pairs analyzed = 115804 no. exposed pairs = 7118 no. arc points = 48782 no. surface atoms = 2393 nbur = 3327 mkacc time = 0.2500000 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 = 1.708000 m= 316 mr = 4689 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 4584 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4666 ## 685 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 12079 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1673796E-10 4.2509059E-11 midg,1,midg; midg,igrid,midg -8.3095766E-11 -4.5916319E-11 1,midg,midg; igrid,midg,midg -1.8856858E-10 4.0319005E-11 gauss-seidel spectral radius is 0.9796773 estimated iterations to convergence 58 setup time was (sec) 0.7400000 now iterating at: 12:39:56 rms-change max change #iterations 6.7624636E-02 11.38769 at 10iterations 3.8902133E-03 0.5503349 at 20iterations 4.5276148E-04 0.1032524 at 30iterations 1.2606682E-04 3.0138016E-02 at 40iterations 3.9884890E-05 9.2430115E-03 at 50iterations finished qdiffx linear iterations at : 12:39:59 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 3.9884890E-05 9.2430115E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 12:39:59 3.386u 0.133s 0:03.85 91.1% 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 Sat Oct 15 2011 at 12:39:59 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 = 5720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.502406 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): 3.820000 74.90600 ymin,ymax (A): 17.62500 84.07500 zmin,zma (A): 6.450000 75.19400 x,y,z range (A): 71.08600 66.45000 68.74400 scale (grids/A): 1.502406 object centre (A): 39.36300 50.85000 40.82200 number of atom coordinates read : 5720 total number of charged atoms : 5550 net assigned charge : -6.999978 assigned positive charge : 858.9704 centred at (gu) : 88.88596 88.01783 87.82665 assigned negative charge : -865.9777 centred at (gu) : 88.73013 88.00808 87.65915 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 102210 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48782 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 28449 mr = 70515 m= 2139 mr = 18600 m= 34 mr = 849 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 667 time to turn everything in is 0.6800000 number of dielectric boundary points 42868 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 716 ## 13 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 41377 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) : 0.5008019 object centre at (A) : 39.36300 50.85000 40.82200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5587484E-02 -9.1329003E-03 midg,1,midg; midg,igrid,midg -5.1516448E-03 -7.2934804E-03 1,midg,midg; igrid,midg,midg -1.0452059E-02 1.9974591E-02 gauss-seidel spectral radius is 0.9981154 estimated iterations to convergence 183 setup time was (sec) 0.9500000 now iterating at: 12:40:01 rms-change max change #iterations 4.059263 165.9809 at 10iterations 1.664826 55.70052 at 20iterations 0.6831999 21.54173 at 30iterations 0.2808525 8.569113 at 40iterations 0.1153117 3.463913 at 50iterations 4.7549892E-02 1.425442 at 60iterations 1.9578271E-02 0.5943756 at 70iterations 8.0882777E-03 0.2548437 at 80iterations 3.3515585E-03 9.6517310E-02 at 90iterations 1.3995201E-03 4.1095734E-02 at 100iterations 5.9149310E-04 1.9966125E-02 at 110iterations 2.5919126E-04 8.8272095E-03 at 120iterations finished qdiffx linear iterations at : 12:40:07 total time elapsed so far: 7.110000 # loops : 120 mean,max change (kT/e) : 2.5919126E-04 8.8272095E-03 energy calculations done at 7.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.280000 DelPhi exited at 12:40:07 7.284u 0.180s 0:07.83 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 Sat Oct 15 2011 at 12:40:07 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 = 5720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.253608 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): 3.820000 74.90600 ymin,ymax (A): 17.62500 84.07500 zmin,zma (A): 6.450000 75.19400 x,y,z range (A): 71.08600 66.45000 68.74400 scale (grids/A): 2.253608 object centre (A): 39.36300 50.85000 40.82200 number of atom coordinates read : 5720 total number of charged atoms : 5550 net assigned charge : -6.999978 assigned positive charge : 858.9704 centred at (gu) : 88.32855 87.02625 86.73937 assigned negative charge : -865.9777 centred at (gu) : 88.09512 87.01229 86.48863 start vw surface at 0.2200000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 238811 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48782 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 104207 mr = 173646 m= 24155 mr = 80894 m= 2963 mr = 17106 m= 120 mr = 1783 m= 0 mr = 37 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 2290 time to turn everything in is 1.660000 number of dielectric boundary points 96790 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 44255 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) : 1.502406 object centre at (A) : 39.36300 50.85000 40.82200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3737237 -0.1786510 midg,1,midg; midg,igrid,midg -0.1002007 -0.1005466 1,midg,midg; igrid,midg,midg -3.1972174E-02 0.5107615 gauss-seidel spectral radius is 0.9991879 estimated iterations to convergence 277 setup time was (sec) 1.950000 now iterating at: 12:40:09 rms-change max change #iterations 11.14571 314.7580 at 10iterations 6.472066 140.5134 at 20iterations 3.726966 86.25970 at 30iterations 2.131151 41.04659 at 40iterations 1.214603 25.83457 at 50iterations 0.6913878 14.88538 at 60iterations 0.3923777 7.259122 at 70iterations 0.2224540 4.491837 at 80iterations 0.1256836 2.206429 at 90iterations 7.0912540E-02 1.294139 at 100iterations 4.0052108E-02 0.7704897 at 110iterations 2.2542130E-02 0.4129448 at 120iterations 1.2715368E-02 0.2428541 at 130iterations 7.1609244E-03 0.1366110 at 140iterations 4.0352535E-03 6.9992065E-02 at 150iterations 2.2792651E-03 3.7536621E-02 at 160iterations 1.2862177E-03 2.2659302E-02 at 170iterations 7.3258765E-04 1.4480591E-02 at 180iterations finished qdiffx linear iterations at : 12:40:19 total time elapsed so far: 11.96000 # loops : 180 mean,max change (kT/e) : 7.3258765E-04 1.4480591E-02 energy calculations done at 11.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.13000 DelPhi exited at 12:40:20 12.131u 0.187s 0:12.60 97.6% 0+0k 0+0io 0pf+0w