Sun Oct 9 08:36:58 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 08:36:58 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 = 6230 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 0.4792805 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): -18.14800 49.83800 ymin,ymax (A): 24.55000 88.08700 zmin,zma (A): -15.66800 58.61000 x,y,z range (A): 67.98599 63.53700 74.27800 scale (grids/A): 0.4792805 object centre (A): 15.84500 56.31850 21.47100 number of atom coordinates read : 6230 total number of charged atoms : 6060 net assigned charge : -5.999979 assigned positive charge : 940.3497 centred at (gu) : 90.37304 89.50423 90.01691 assigned negative charge : -946.3585 centred at (gu) : 90.33581 89.50474 90.10377 start vw surface at 0.2500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 8923 nv = 96 ne = 84 npr = 124980 no. pairs analyzed = 124980 no. exposed pairs = 7720 no. arc points = 53707 no. surface atoms = 2585 nbur = 3645 mkacc time = 0.3500000 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 = 1.792000 m= 273 mr = 4565 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 4630 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5034 ## 878 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 12096 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1279671E-11 -9.2468450E-11 midg,1,midg; midg,igrid,midg -2.1684852E-11 -1.7297361E-11 1,midg,midg; igrid,midg,midg -4.5327166E-11 1.2586761E-11 gauss-seidel spectral radius is 0.9778541 estimated iterations to convergence 56 setup time was (sec) 0.9500000 now iterating at: 08:36:59 rms-change max change #iterations 5.6787167E-02 8.783161 at 10iterations 2.9086971E-03 0.4688683 at 20iterations 3.2641113E-04 7.0816040E-02 at 30iterations 8.1295715E-05 1.6757965E-02 at 40iterations 2.4205929E-05 4.3487549E-03 at 50iterations finished qdiffx linear iterations at : 08:37:02 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 2.4205929E-05 4.3487549E-03 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.450000 DelPhi exited at 08:37:03 4.453u 0.268s 0:05.05 93.2% 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 08:37:03 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 = 6230 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 1.437842 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): -18.14800 49.83800 ymin,ymax (A): 24.55000 88.08700 zmin,zma (A): -15.66800 58.61000 x,y,z range (A): 67.98599 63.53700 74.27800 scale (grids/A): 1.437842 object centre (A): 15.84500 56.31850 21.47100 number of atom coordinates read : 6230 total number of charged atoms : 6060 net assigned charge : -5.999979 assigned positive charge : 940.3497 centred at (gu) : 91.11653 88.51053 90.04887 assigned negative charge : -946.3585 centred at (gu) : 91.00703 88.51411 90.31126 start vw surface at 0.2700000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 101953 reading accessible surface arcs data from file ARCDAT no. of arc points read = 53707 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 28387 mr = 69842 m= 2026 mr = 18338 m= 29 mr = 709 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9500000 number of dielectric boundary points 43506 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 874 ## 19 charges are in solution ## iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 44497 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) : 0.4792805 object centre at (A) : 15.84500 56.31850 21.47100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1898482E-03 -7.2561204E-03 midg,1,midg; midg,igrid,midg -4.6820575E-03 -1.5550866E-03 1,midg,midg; igrid,midg,midg 8.7724859E-04 -5.3202495E-04 gauss-seidel spectral radius is 0.9979587 estimated iterations to convergence 176 setup time was (sec) 1.260000 now iterating at: 08:37:04 rms-change max change #iterations 3.832516 154.4497 at 10iterations 1.514898 53.53884 at 20iterations 0.6028027 18.75828 at 30iterations 0.2381409 8.663792 at 40iterations 9.4493791E-02 2.960449 at 50iterations 3.7505869E-02 1.197089 at 60iterations 1.4905207E-02 0.4567871 at 70iterations 5.9378035E-03 0.1820335 at 80iterations 2.3797303E-03 8.3038330E-02 at 90iterations 9.6152443E-04 3.3428192E-02 at 100iterations 3.9981096E-04 1.3000488E-02 at 110iterations 1.7462208E-04 7.2684288E-03 at 120iterations finished qdiffx linear iterations at : 08:37:13 total time elapsed so far: 9.740000 # loops : 120 mean,max change (kT/e) : 1.7462208E-04 7.2684288E-03 energy calculations done at 9.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.920000 DelPhi exited at 08:37:13 9.918u 0.283s 0:10.52 96.8% 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 08:37:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6230 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 2.156762 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): -18.14800 49.83800 ymin,ymax (A): 24.55000 88.08700 zmin,zma (A): -15.66800 58.61000 x,y,z range (A): 67.98599 63.53700 74.27800 scale (grids/A): 2.156762 object centre (A): 15.84500 56.31850 21.47100 number of atom coordinates read : 6230 total number of charged atoms : 6060 net assigned charge : -5.999979 assigned positive charge : 940.3497 centred at (gu) : 91.67424 87.76535 90.07253 assigned negative charge : -946.3585 centred at (gu) : 91.51054 87.77113 90.46689 start vw surface at 0.2600000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 238297 reading accessible surface arcs data from file ARCDAT no. of arc points read = 53707 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 103887 mr = 172317 m= 23888 mr = 80046 m= 2667 mr = 16731 m= 77 mr = 1442 m= 0 mr = 8 time to grow re-entrant surface = 1.390000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.250000 number of dielectric boundary points 98272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 151 iepsmp to db, and charging done at 2.410000 number of grid points assigned charge 48224 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) : 1.437842 object centre at (A) : 15.84500 56.31850 21.47100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8065189E-02 0.1982206 midg,1,midg; midg,igrid,midg -9.6714735E-02 -1.9559568E-02 1,midg,midg; igrid,midg,midg 5.9989534E-02 5.7322886E-03 gauss-seidel spectral radius is 0.9991504 estimated iterations to convergence 271 setup time was (sec) 2.580000 now iterating at: 08:37:16 rms-change max change #iterations 10.84314 283.3189 at 10iterations 6.210299 141.5218 at 20iterations 3.540540 84.82164 at 30iterations 2.008513 42.33812 at 40iterations 1.132863 22.58064 at 50iterations 0.6367468 11.57152 at 60iterations 0.3585191 8.062463 at 70iterations 0.2007441 4.095329 at 80iterations 0.1122602 2.372668 at 90iterations 6.2642545E-02 1.452338 at 100iterations 3.4987640E-02 0.7191277 at 110iterations 1.9501906E-02 0.3812761 at 120iterations 1.0891194E-02 0.1972365 at 130iterations 6.0506957E-03 0.1092014 at 140iterations 3.3751505E-03 6.9296837E-02 at 150iterations 1.8797660E-03 3.3400059E-02 at 160iterations 1.0485039E-03 1.9844055E-02 at 170iterations 5.8517087E-04 1.0807991E-02 at 180iterations finished qdiffx linear iterations at : 08:37:30 total time elapsed so far: 16.92000 # loops : 180 mean,max change (kT/e) : 5.8517087E-04 1.0807991E-02 energy calculations done at 16.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.10000 DelPhi exited at 08:37:31 17.099u 0.328s 0:17.69 98.4% 0+0k 0+0io 0pf+0w