Sat Oct 8 18:22:18 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 8 2011 at 18:22:18 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3776 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5512713 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): -1.926000 60.42600 ymin,ymax (A): -18.55100 44.92300 zmin,zma (A): -5.634000 58.94400 x,y,z range (A): 62.35200 63.47400 64.57800 scale (grids/A): 0.5512713 object centre (A): 29.25000 13.18600 26.65500 number of atom coordinates read : 3776 total number of charged atoms : 3626 net assigned charge : -7.499981 assigned positive charge : 569.6973 centred at (gu) : 88.84008 86.57981 90.53008 assigned negative charge : -577.1998 centred at (gu) : 88.89748 86.57845 90.52471 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7524 nv = 96 ne = 84 npr = 75709 no. pairs analyzed = 75709 no. exposed pairs = 4879 no. arc points = 34480 no. surface atoms = 1629 nbur = 2147 mkacc time = 0.1600000 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 = 1.568000 m= 331 mr = 3882 m= 0 mr = 9 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3448 ## 412 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9831 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5225990E-10 -5.8511018E-10 midg,1,midg; midg,igrid,midg -1.3444729E-09 -2.5109845E-10 1,midg,midg; igrid,midg,midg 3.2491031E-11 -8.8160840E-10 gauss-seidel spectral radius is 0.9830964 estimated iterations to convergence 63 setup time was (sec) 0.6300000 now iterating at: 18:22:19 rms-change max change #iterations 8.5012861E-02 14.22696 at 10iterations 6.0882219E-03 0.9212189 at 20iterations 5.3783506E-04 8.1130981E-02 at 30iterations 1.0289597E-04 1.4975548E-02 at 40iterations 2.9482439E-05 3.9615631E-03 at 50iterations finished qdiffx linear iterations at : 18:22:21 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 2.9482439E-05 3.9615631E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 18:22:22 3.469u 0.207s 0:03.95 92.6% 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 8 2011 at 18:22:22 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 = 3776 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: 1.653814 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): -1.926000 60.42600 ymin,ymax (A): -18.55100 44.92300 zmin,zma (A): -5.634000 58.94400 x,y,z range (A): 62.35200 63.47400 64.57800 scale (grids/A): 1.653814 object centre (A): 29.25000 13.18600 26.65500 number of atom coordinates read : 3776 total number of charged atoms : 3626 net assigned charge : -7.499981 assigned positive charge : 569.6973 centred at (gu) : 86.51898 79.73823 91.58862 assigned negative charge : -577.1998 centred at (gu) : 86.69189 79.73500 91.57394 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 83075 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34480 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 26132 mr = 56362 m= 2710 mr = 17718 m= 83 mr = 1220 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.5800000 number of dielectric boundary points 36694 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 417 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 27844 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) : 0.5512713 object centre at (A) : 29.25000 13.18600 26.65500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6529490E-03 -1.3833742E-03 midg,1,midg; midg,igrid,midg -2.3455286E-02 -8.2928948E-03 1,midg,midg; igrid,midg,midg -1.0330616E-02 -3.0265093E-02 gauss-seidel spectral radius is 0.9983069 estimated iterations to convergence 193 setup time was (sec) 0.8800000 now iterating at: 18:22:23 rms-change max change #iterations 3.915723 168.6228 at 10iterations 1.676393 59.84178 at 20iterations 0.7213231 24.17403 at 30iterations 0.3096583 9.720655 at 40iterations 0.1326758 4.130769 at 50iterations 5.7332505E-02 1.901516 at 60iterations 2.4560552E-02 0.7632608 at 70iterations 1.0613324E-02 0.3561592 at 80iterations 4.5670336E-03 0.1538885 at 90iterations 1.9813115E-03 6.7420959E-02 at 100iterations 8.6889719E-04 2.7088165E-02 at 110iterations 3.9107166E-04 1.2646198E-02 at 120iterations finished qdiffx linear iterations at : 18:22:30 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 3.9107166E-04 1.2646198E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 18:22:30 7.568u 0.230s 0:08.11 96.0% 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 Sat Oct 8 2011 at 18:22:30 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 = 3776 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.480721 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): -1.926000 60.42600 ymin,ymax (A): -18.55100 44.92300 zmin,zma (A): -5.634000 58.94400 x,y,z range (A): 62.35200 63.47400 64.57800 scale (grids/A): 2.480721 object centre (A): 29.25000 13.18600 26.65500 number of atom coordinates read : 3776 total number of charged atoms : 3626 net assigned charge : -7.499981 assigned positive charge : 569.6973 centred at (gu) : 84.77818 74.60701 92.38249 assigned negative charge : -577.1998 centred at (gu) : 85.03772 74.60230 92.36086 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 192821 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34480 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 89646 mr = 137680 m= 25757 mr = 70503 m= 4283 mr = 19111 m= 263 mr = 2648 m= 8 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 176 time to turn everything in is 1.390000 number of dielectric boundary points 82744 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 28976 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) : 1.653814 object centre at (A) : 29.25000 13.18600 26.65500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7681563E-02 0.1851708 midg,1,midg; midg,igrid,midg -0.3491137 -0.1030255 1,midg,midg; igrid,midg,midg -0.1476485 -0.5584096 gauss-seidel spectral radius is 0.9991921 estimated iterations to convergence 278 setup time was (sec) 1.720000 now iterating at: 18:22:32 rms-change max change #iterations 10.09940 328.9490 at 10iterations 5.769032 139.8135 at 20iterations 3.288307 69.07289 at 30iterations 1.864243 38.30883 at 40iterations 1.054691 22.73690 at 50iterations 0.5945470 12.40358 at 60iterations 0.3343821 6.721333 at 70iterations 0.1882612 3.556791 at 80iterations 0.1058920 1.985002 at 90iterations 5.9314288E-02 1.261843 at 100iterations 3.3334363E-02 0.6568995 at 110iterations 1.8720042E-02 0.3580117 at 120iterations 1.0494638E-02 0.1981125 at 130iterations 5.8878167E-03 0.1036267 at 140iterations 3.3194250E-03 6.6890717E-02 at 150iterations 1.8664679E-03 3.4042358E-02 at 160iterations 1.0578502E-03 2.0611763E-02 at 170iterations 6.0253643E-04 1.2747765E-02 at 180iterations finished qdiffx linear iterations at : 18:22:43 total time elapsed so far: 12.29000 # loops : 180 mean,max change (kT/e) : 6.0253643E-04 1.2747765E-02 energy calculations done at 12.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.48000 DelPhi exited at 18:22:43 12.479u 0.246s 0:12.99 97.8% 0+0k 0+0io 0pf+0w