Sat Oct 8 18:22:43 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 Sat Oct 8 2011 at 18:22:43 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: 300 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= 0.1100000 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 : 576.4973 centred at (gu) : 88.83106 86.60614 90.50203 assigned negative charge : -583.9999 centred at (gu) : 88.88847 86.60981 90.49331 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 = 0.1700000 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 = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 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 0.4800000 number of grid points assigned charge 9831 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8971827E-10 -5.4355792E-10 midg,1,midg; midg,igrid,midg -1.2171548E-09 -2.7656014E-10 1,midg,midg; igrid,midg,midg 3.8981957E-11 -8.8701568E-10 gauss-seidel spectral radius is 0.9830964 estimated iterations to convergence 63 setup time was (sec) 0.6000000 now iterating at: 18:22:44 rms-change max change #iterations 8.8588782E-02 14.16467 at 10iterations 6.2741535E-03 0.9116268 at 20iterations 5.1746785E-04 7.7407837E-02 at 30iterations 8.9170411E-05 1.3299942E-02 at 40iterations 2.4565654E-05 3.5104752E-03 at 50iterations finished qdiffx linear iterations at : 18:22:47 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 2.4565654E-05 3.5104752E-03 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 18:22:47 3.232u 0.143s 0:03.74 90.1% 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 8 2011 at 18:22:47 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: 300 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 : 576.4973 centred at (gu) : 86.49201 79.81728 91.50448 assigned negative charge : -583.9999 centred at (gu) : 86.66495 79.82912 91.47980 start vw surface at 0.1900000 fill in re-entrant regions at 0.2800000 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 0.7000000 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 -1.8749450E-03 -1.2518740E-03 midg,1,midg; midg,igrid,midg -2.2515137E-02 -8.6757811E-03 1,midg,midg; igrid,midg,midg -1.0031818E-02 -2.9803909E-02 gauss-seidel spectral radius is 0.9983069 estimated iterations to convergence 193 setup time was (sec) 0.8500000 now iterating at: 18:22:48 rms-change max change #iterations 3.981837 168.6228 at 10iterations 1.704838 59.84177 at 20iterations 0.7335908 24.17402 at 30iterations 0.3148442 9.930712 at 40iterations 0.1348770 4.195637 at 50iterations 5.8298945E-02 1.954098 at 60iterations 2.4964092E-02 0.7853458 at 70iterations 1.0781294E-02 0.3670731 at 80iterations 4.6372400E-03 0.1613024 at 90iterations 2.0078009E-03 6.5872192E-02 at 100iterations 8.7689084E-04 2.8362274E-02 at 110iterations 3.9084605E-04 1.2826204E-02 at 120iterations finished qdiffx linear iterations at : 18:22:54 total time elapsed so far: 6.890000 # loops : 120 mean,max change (kT/e) : 3.9084605E-04 1.2826204E-02 energy calculations done at 6.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.060000 DelPhi exited at 18:22:55 7.064u 0.168s 0:07.52 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 18:22:55 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: 300 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: 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 : 576.4973 centred at (gu) : 84.73774 74.72563 92.25629 assigned negative charge : -583.9999 centred at (gu) : 84.99732 74.74351 92.21967 start vw surface at 0.1700000 fill in re-entrant regions at 0.4600000 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 = 0.8200000 no. cavity mid-points inaccessible to solvent = 176 time to turn everything in is 1.400000 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 1.5116665E-02 0.1863068 midg,1,midg; midg,igrid,midg -0.3366638 -0.1084324 1,midg,midg; igrid,midg,midg -0.1452966 -0.5510152 gauss-seidel spectral radius is 0.9991921 estimated iterations to convergence 278 setup time was (sec) 1.680000 now iterating at: 18:22:57 rms-change max change #iterations 10.24313 328.9635 at 10iterations 5.847356 139.7977 at 20iterations 3.332594 72.03241 at 30iterations 1.888508 38.97120 at 40iterations 1.068028 23.03735 at 50iterations 0.6019897 12.52222 at 60iterations 0.3385571 6.656574 at 70iterations 0.1904825 3.612188 at 80iterations 0.1071557 1.941323 at 90iterations 6.0007572E-02 1.287409 at 100iterations 3.3726476E-02 0.6479468 at 110iterations 1.8938726E-02 0.3510227 at 120iterations 1.0613626E-02 0.1982040 at 130iterations 5.9555392E-03 0.1039214 at 140iterations 3.3559795E-03 6.7754269E-02 at 150iterations 1.8865076E-03 3.4503937E-02 at 160iterations 1.0692719E-03 2.0620465E-02 at 170iterations 6.0928980E-04 1.2679100E-02 at 180iterations finished qdiffx linear iterations at : 18:23:06 total time elapsed so far: 11.26000 # loops : 180 mean,max change (kT/e) : 6.0928980E-04 1.2679100E-02 energy calculations done at 11.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.43000 DelPhi exited at 18:23:07 11.436u 0.183s 0:11.90 97.5% 0+0k 0+0io 0pf+0w