Sun Oct 9 08:12:41 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 Sun Oct 9 2011 at 08:12:41 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3455 !!! WARNING: NAP 1040 has a net charge of -2.0000 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: 0.5332295 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): -24.81300 22.07600 ymin,ymax (A): -22.24800 36.27500 zmin,zma (A): -16.06400 50.69900 x,y,z range (A): 46.88900 58.52300 66.76300 scale (grids/A): 0.5332295 object centre (A): -1.368500 7.013501 17.31750 number of atom coordinates read : 3455 total number of charged atoms : 3313 net assigned charge : 8.500021 assigned positive charge : 520.4196 centred at (gu) : 89.65505 87.27315 90.05727 assigned negative charge : -511.9211 centred at (gu) : 89.72600 87.30067 90.16436 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6403 nv = 96 ne = 84 npr = 68431 no. pairs analyzed = 68431 no. exposed pairs = 4627 no. arc points = 33371 no. surface atoms = 1526 nbur = 1929 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 = 1.596000 m= 260 mr = 3113 m= 0 mr = 3 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3547 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3278 ## 451 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8439 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.8991574E-10 -1.9812922E-10 midg,1,midg; midg,igrid,midg 8.7233581E-10 9.6064330E-11 1,midg,midg; igrid,midg,midg 6.9491191E-10 -1.9849528E-11 gauss-seidel spectral radius is 0.9819199 estimated iterations to convergence 61 setup time was (sec) 0.4300000 now iterating at: 08:12:42 rms-change max change #iterations 7.0220590E-02 11.70845 at 10iterations 4.4376934E-03 0.8186836 at 20iterations 4.1821814E-04 6.3556671E-02 at 30iterations 9.0346635E-05 1.1610031E-02 at 40iterations 2.5082703E-05 3.2062531E-03 at 50iterations finished qdiffx linear iterations at : 08:12:45 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 2.5082703E-05 3.2062531E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 08:12:45 3.446u 0.171s 0:03.90 92.5% 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 Sun Oct 9 2011 at 08:12:45 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3455 !!! WARNING: NAP 1040 has a net charge of -2.0000 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: 1.599688 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): -24.81300 22.07600 ymin,ymax (A): -22.24800 36.27500 zmin,zma (A): -16.06400 50.69900 x,y,z range (A): 46.88900 58.52300 66.76300 scale (grids/A): 1.599688 object centre (A): -1.368500 7.013501 17.31750 number of atom coordinates read : 3455 total number of charged atoms : 3313 net assigned charge : 8.500021 assigned positive charge : 520.4196 centred at (gu) : 88.96420 81.81850 90.17089 assigned negative charge : -511.9211 centred at (gu) : 89.17781 81.90178 90.49284 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70649 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33371 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21785 mr = 46398 m= 2197 mr = 14320 m= 63 mr = 970 m= 0 mr = 2 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 909 time to turn everything in is 0.3500000 number of dielectric boundary points 33004 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 358 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 25240 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) : 0.5332295 object centre at (A) : -1.368500 7.013501 17.31750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8011402E-02 -1.1328666E-02 midg,1,midg; midg,igrid,midg 1.4829425E-02 1.0310490E-02 1,midg,midg; igrid,midg,midg 1.0758021E-02 -4.6192601E-04 gauss-seidel spectral radius is 0.9981679 estimated iterations to convergence 186 setup time was (sec) 0.5700000 now iterating at: 08:12:46 rms-change max change #iterations 3.454976 162.4446 at 10iterations 1.426242 52.16591 at 20iterations 0.5933297 20.30271 at 30iterations 0.2461869 10.31027 at 40iterations 0.1021224 3.724655 at 50iterations 4.2496443E-02 1.462433 at 60iterations 1.7654965E-02 0.6074533 at 70iterations 7.3424438E-03 0.2637691 at 80iterations 3.0866326E-03 0.1088085 at 90iterations 1.2919679E-03 4.6619415E-02 at 100iterations 5.4808613E-04 1.8600464E-02 at 110iterations 2.3971735E-04 9.9277496E-03 at 120iterations finished qdiffx linear iterations at : 08:12:53 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 2.3971735E-04 9.9277496E-03 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 08:12:53 7.773u 0.199s 0:08.26 96.3% 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 08:12:53 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3455 !!! WARNING: NAP 1040 has a net charge of -2.0000 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: 2.399533 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): -24.81300 22.07600 ymin,ymax (A): -22.24800 36.27500 zmin,zma (A): -16.06400 50.69900 x,y,z range (A): 46.88900 58.52300 66.76300 scale (grids/A): 2.399533 object centre (A): -1.368500 7.013501 17.31750 number of atom coordinates read : 3455 total number of charged atoms : 3313 net assigned charge : 8.500021 assigned positive charge : 520.4196 centred at (gu) : 88.44623 77.72746 90.25621 assigned negative charge : -511.9211 centred at (gu) : 88.76642 77.85241 90.73927 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 164218 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33371 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 74789 mr = 114359 m= 21246 mr = 57387 m= 3365 mr = 15393 m= 229 mr = 2071 m= 7 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 3200 time to turn everything in is 0.8400000 number of dielectric boundary points 74567 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 26455 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) : 1.599688 object centre at (A) : -1.368500 7.013501 17.31750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2666076 -0.3058667 midg,1,midg; midg,igrid,midg 0.2778283 0.1997566 1,midg,midg; igrid,midg,midg 0.1385829 -2.7809095E-02 gauss-seidel spectral radius is 0.9991517 estimated iterations to convergence 271 setup time was (sec) 1.080000 now iterating at: 08:12:55 rms-change max change #iterations 9.234092 273.4201 at 10iterations 5.288423 142.9946 at 20iterations 3.011092 86.51686 at 30iterations 1.695571 44.06513 at 40iterations 0.9485750 21.83366 at 50iterations 0.5311184 13.51970 at 60iterations 0.2951882 6.903016 at 70iterations 0.1647454 4.381857 at 80iterations 9.1545716E-02 2.441780 at 90iterations 5.0715972E-02 1.116950 at 100iterations 2.8191717E-02 0.7050323 at 110iterations 1.5588786E-02 0.3528748 at 120iterations 8.6298063E-03 0.2313038 at 130iterations 4.7798785E-03 0.1096191 at 140iterations 2.6398816E-03 5.5236816E-02 at 150iterations 1.4605747E-03 3.2230377E-02 at 160iterations 8.0898439E-04 1.7765045E-02 at 170iterations 4.4658696E-04 9.4547272E-03 at 180iterations finished qdiffx linear iterations at : 08:13:06 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 4.4658696E-04 9.4547272E-03 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 08:13:06 12.474u 0.217s 0:12.99 97.6% 0+0k 0+0io 0pf+0w