Sun Oct 9 22:42:06 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 22:42:06 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 = 2751 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: 0.5948105 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): -61.85900 -3.292000 ymin,ymax (A): -32.29200 20.12700 zmin,zma (A): 11.91400 71.76500 x,y,z range (A): 58.56700 52.41900 59.85100 scale (grids/A): 0.5948105 object centre (A): -32.57550 -6.082500 41.83950 number of atom coordinates read : 2751 total number of charged atoms : 2605 net assigned charge : 7.500013 assigned positive charge : 417.9635 centred at (gu) : 89.91268 90.29560 90.62535 assigned negative charge : -410.4645 centred at (gu) : 89.98186 90.27637 90.69250 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6314 nv = 96 ne = 84 npr = 54643 no. pairs analyzed = 54643 no. exposed pairs = 3426 no. arc points = 24411 no. surface atoms = 1153 nbur = 1598 mkacc time = 0.1200000 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 = 1.456000 m= 286 mr = 3231 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.3000000 number of dielectric boundary points 3337 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2512 ## 261 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8035 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2628834E-09 5.5651805E-10 midg,1,midg; midg,igrid,midg 1.9597710E-09 3.5813910E-09 1,midg,midg; igrid,midg,midg 5.0742299E-09 4.2727943E-10 gauss-seidel spectral radius is 0.9853879 estimated iterations to convergence 68 setup time was (sec) 0.5000000 now iterating at: 22:42:07 rms-change max change #iterations 0.1030640 17.87505 at 10iterations 8.7071275E-03 1.284496 at 20iterations 7.1643636E-04 0.1074123 at 30iterations 5.9909406E-05 9.0277195E-03 at 40iterations 5.1032780E-06 9.4532967E-04 at 50iterations finished qdiffx linear iterations at : 22:42:09 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 5.1032780E-06 9.4532967E-04 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 22:42:10 3.076u 0.149s 0:03.62 88.6% 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 Sun Oct 9 2011 at 22:42:10 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 = 2751 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.784431 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): -61.85900 -3.292000 ymin,ymax (A): -32.29200 20.12700 zmin,zma (A): 11.91400 71.76500 x,y,z range (A): 58.56700 52.41900 59.85100 scale (grids/A): 1.784431 object centre (A): -32.57550 -6.082500 41.83950 number of atom coordinates read : 2751 total number of charged atoms : 2605 net assigned charge : 7.500013 assigned positive charge : 417.9635 centred at (gu) : 89.73735 90.88620 91.87519 assigned negative charge : -410.4645 centred at (gu) : 89.94537 90.82893 92.07713 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 68906 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24411 grid for indexing accessible points = 1.400000 m= 21629 mr = 46141 m= 2842 mr = 15039 m= 148 mr = 1698 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1006 time to turn everything in is 0.4600000 number of dielectric boundary points 30608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 211 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 20278 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) : 0.5948105 object centre at (A) : -32.57550 -6.082500 41.83950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7354935E-03 6.6918479E-03 midg,1,midg; midg,igrid,midg 6.2129861E-03 2.1815766E-03 1,midg,midg; igrid,midg,midg 8.6862333E-03 1.7720185E-02 gauss-seidel spectral radius is 0.9984617 estimated iterations to convergence 202 setup time was (sec) 0.7200000 now iterating at: 22:42:10 rms-change max change #iterations 3.817378 184.3556 at 10iterations 1.698130 62.65768 at 20iterations 0.7521563 25.77793 at 30iterations 0.3372318 10.67823 at 40iterations 0.1504576 5.248596 at 50iterations 6.7086585E-02 2.391613 at 60iterations 2.9921524E-02 1.056890 at 70iterations 1.3408223E-02 0.4565315 at 80iterations 5.9739486E-03 0.1868801 at 90iterations 2.6767703E-03 9.5413208E-02 at 100iterations 1.1944128E-03 4.4078827E-02 at 110iterations 5.3382234E-04 1.8261433E-02 at 120iterations finished qdiffx linear iterations at : 22:42:16 total time elapsed so far: 6.730000 # loops : 120 mean,max change (kT/e) : 5.3382234E-04 1.8261433E-02 energy calculations done at 6.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.900000 DelPhi exited at 22:42:17 6.899u 0.178s 0:07.39 95.5% 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 22:42:17 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 = 2751 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.676647 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): -61.85900 -3.292000 ymin,ymax (A): -32.29200 20.12700 zmin,zma (A): 11.91400 71.76500 x,y,z range (A): 58.56700 52.41900 59.85100 scale (grids/A): 2.676647 object centre (A): -32.57550 -6.082500 41.83950 number of atom coordinates read : 2751 total number of charged atoms : 2605 net assigned charge : 7.500013 assigned positive charge : 417.9635 centred at (gu) : 89.60592 91.32899 92.81252 assigned negative charge : -410.4645 centred at (gu) : 89.91801 91.24343 93.11564 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 159673 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24411 grid for indexing accessible points = 1.400000 m= 73067 mr = 112482 m= 22752 mr = 57993 m= 4927 mr = 17467 m= 601 mr = 3615 m= 30 mr = 384 m= 0 mr = 17 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 3661 time to turn everything in is 1.140000 number of dielectric boundary points 69092 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 20832 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) : 1.784431 object centre at (A) : -32.57550 -6.082500 41.83950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2340140 -0.2338077 midg,1,midg; midg,igrid,midg 0.1029849 -2.6212020E-02 1,midg,midg; igrid,midg,midg -9.8733224E-02 0.2628187 gauss-seidel spectral radius is 0.9992125 estimated iterations to convergence 281 setup time was (sec) 1.420000 now iterating at: 22:42:19 rms-change max change #iterations 9.263177 310.7963 at 10iterations 5.316943 121.6680 at 20iterations 3.020339 74.28403 at 30iterations 1.713619 38.24835 at 40iterations 0.9706916 19.94525 at 50iterations 0.5486802 13.78830 at 60iterations 0.3099931 6.253086 at 70iterations 0.1751757 3.809708 at 80iterations 9.8734483E-02 2.098326 at 90iterations 5.5607699E-02 1.086487 at 100iterations 3.1450581E-02 0.6138790 at 110iterations 1.7705608E-02 0.3781643 at 120iterations 9.9938018E-03 0.1875362 at 130iterations 5.6257453E-03 0.1186314 at 140iterations 3.1745236E-03 6.3312531E-02 at 150iterations 1.7847929E-03 3.3397675E-02 at 160iterations 1.0079085E-03 1.9636154E-02 at 170iterations 5.6895940E-04 1.0794640E-02 at 180iterations finished qdiffx linear iterations at : 22:42:28 total time elapsed so far: 10.96000 # loops : 180 mean,max change (kT/e) : 5.6895940E-04 1.0794640E-02 energy calculations done at 10.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.13000 DelPhi exited at 22:42:29 11.136u 0.177s 0:11.64 97.0% 0+0k 0+0io 0pf+0w