Mon Oct 10 17:00:56 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 Mon Oct 10 2011 at 17:00:57 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4139 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5153445 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): -15.19200 36.65800 ymin,ymax (A): -30.61300 31.39800 zmin,zma (A): -4.001000 65.07900 x,y,z range (A): 51.85000 62.01100 69.08000 scale (grids/A): 0.5153445 object centre (A): 10.73300 0.3924990 30.53900 number of atom coordinates read : 4139 total number of charged atoms : 3897 net assigned charge : 5.300024 assigned positive charge : 614.2618 centred at (gu) : 90.18869 90.55000 87.09306 assigned negative charge : -608.9651 centred at (gu) : 90.05344 90.61026 87.08509 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 6926 nv = 96 ne = 84 npr = 84375 no. pairs analyzed = 84375 no. exposed pairs = 5329 no. arc points = 37296 no. surface atoms = 1766 nbur = 2373 mkacc time = 0.2300000 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 = 1.652000 m= 242 mr = 3528 m= 0 mr = 9 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 3631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3503 ## 531 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 9187 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5009674E-10 5.4937978E-11 midg,1,midg; midg,igrid,midg 2.1895027E-10 -8.1023944E-11 1,midg,midg; igrid,midg,midg -2.6142374E-10 4.7068538E-10 gauss-seidel spectral radius is 0.9806966 estimated iterations to convergence 59 setup time was (sec) 0.8400000 now iterating at: 17:00:58 rms-change max change #iterations 6.6197403E-02 13.21799 at 10iterations 3.9044712E-03 0.6953354 at 20iterations 3.8051896E-04 5.9722900E-02 at 30iterations 1.0476989E-04 1.4490008E-02 at 40iterations 3.5498044E-05 5.3977966E-03 at 50iterations finished qdiffx linear iterations at : 17:01:01 total time elapsed so far: 4.340000 # loops : 50 mean,max change (kT/e) : 3.5498044E-05 5.3977966E-03 energy calculations done at 4.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 17:01:02 4.532u 0.270s 0:05.46 87.9% 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 17:01:02 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4139 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.546034 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): -15.19200 36.65800 ymin,ymax (A): -30.61300 31.39800 zmin,zma (A): -4.001000 65.07900 x,y,z range (A): 51.85000 62.01100 69.08000 scale (grids/A): 1.546034 object centre (A): 10.73300 0.3924990 30.53900 number of atom coordinates read : 4139 total number of charged atoms : 3897 net assigned charge : 5.300024 assigned positive charge : 614.2618 centred at (gu) : 90.56479 91.64874 81.27773 assigned negative charge : -608.9651 centred at (gu) : 90.16017 91.83038 81.25509 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 77824 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37296 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 22379 mr = 52485 m= 2044 mr = 14793 m= 45 mr = 930 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 72 time to turn everything in is 0.6700000 number of dielectric boundary points 34084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 488 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 29376 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) : 0.5153445 object centre at (A) : 10.73300 0.3924990 30.53900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2777321E-03 1.0533835E-02 midg,1,midg; midg,igrid,midg -4.7027439E-04 -1.0836378E-02 1,midg,midg; igrid,midg,midg -2.2398224E-03 1.1484683E-02 gauss-seidel spectral radius is 0.9980892 estimated iterations to convergence 182 setup time was (sec) 1.000000 now iterating at: 17:01:03 rms-change max change #iterations 3.512075 179.6706 at 10iterations 1.421471 53.33979 at 20iterations 0.5814071 19.46323 at 30iterations 0.2358398 8.694939 at 40iterations 9.6459374E-02 3.475092 at 50iterations 3.9318103E-02 1.264229 at 60iterations 1.6024878E-02 0.5576630 at 70iterations 6.5639112E-03 0.2116666 at 80iterations 2.6976331E-03 9.7724915E-02 at 90iterations 1.1165455E-03 3.8181305E-02 at 100iterations 4.7017523E-04 1.7907619E-02 at 110iterations 2.0785327E-04 7.2841644E-03 at 120iterations finished qdiffx linear iterations at : 17:01:12 total time elapsed so far: 9.380000 # loops : 120 mean,max change (kT/e) : 2.0785327E-04 7.2841644E-03 energy calculations done at 9.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.570000 DelPhi exited at 17:01:12 9.571u 0.245s 0:10.16 96.5% 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 17:01:13 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4139 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.319050 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): -15.19200 36.65800 ymin,ymax (A): -30.61300 31.39800 zmin,zma (A): -4.001000 65.07900 x,y,z range (A): 51.85000 62.01100 69.08000 scale (grids/A): 2.319050 object centre (A): 10.73300 0.3924990 30.53900 number of atom coordinates read : 4139 total number of charged atoms : 3897 net assigned charge : 5.300024 assigned positive charge : 614.2618 centred at (gu) : 90.84692 92.47286 76.91623 assigned negative charge : -608.9651 centred at (gu) : 90.24004 92.74566 76.88268 start vw surface at 0.1700000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 181232 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37296 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 80110 mr = 129136 m= 20620 mr = 62276 m= 3077 mr = 14788 m= 152 mr = 1936 m= 4 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 243 time to turn everything in is 1.410000 number of dielectric boundary points 76999 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 31104 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) : 1.546034 object centre at (A) : 10.73300 0.3924990 30.53900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1697847 0.2866914 midg,1,midg; midg,igrid,midg -9.6774064E-02 -0.2399463 1,midg,midg; igrid,midg,midg -3.1602941E-02 0.1696636 gauss-seidel spectral radius is 0.9991416 estimated iterations to convergence 270 setup time was (sec) 1.750000 now iterating at: 17:01:15 rms-change max change #iterations 9.500979 303.4306 at 10iterations 5.412086 148.6094 at 20iterations 3.050153 73.62180 at 30iterations 1.715040 39.02799 at 40iterations 0.9606237 24.49157 at 50iterations 0.5350586 12.68780 at 60iterations 0.2980478 7.284086 at 70iterations 0.1654255 3.654817 at 80iterations 9.1695666E-02 2.051611 at 90iterations 5.0860140E-02 1.073501 at 100iterations 2.8066322E-02 0.6933594 at 110iterations 1.5506126E-02 0.3208517 at 120iterations 8.5998103E-03 0.1764908 at 130iterations 4.7437921E-03 9.2861176E-02 at 140iterations 2.6144460E-03 4.9154282E-02 at 150iterations 1.4434656E-03 2.8900146E-02 at 160iterations 7.9705706E-04 1.4961243E-02 at 170iterations 4.3998417E-04 9.5868111E-03 at 180iterations finished qdiffx linear iterations at : 17:01:28 total time elapsed so far: 15.17000 # loops : 180 mean,max change (kT/e) : 4.3998417E-04 9.5868111E-03 energy calculations done at 15.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.36000 DelPhi exited at 17:01:29 15.357u 0.275s 0:16.54 94.4% 0+0k 0+0io 0pf+0w