Mon Oct 10 16:20:58 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 Mon Oct 10 2011 at 16:20:58 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 = 4641 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: 0.5514848 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): -63.08400 -7.478000 ymin,ymax (A): -34.76000 29.79300 zmin,zma (A): -29.23600 33.33700 x,y,z range (A): 55.60600 64.55300 62.57300 scale (grids/A): 0.5514848 object centre (A): -35.28100 -2.483501 2.050499 number of atom coordinates read : 4641 total number of charged atoms : 4483 net assigned charge : 6.000029 assigned positive charge : 696.0182 centred at (gu) : 90.35304 90.17496 88.73385 assigned negative charge : -690.0222 centred at (gu) : 90.36518 90.20919 88.74734 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 9099 nv = 96 ne = 84 npr = 94780 no. pairs analyzed = 94780 no. exposed pairs = 5682 no. arc points = 38638 no. surface atoms = 1924 nbur = 2717 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 = 1.540000 m= 365 mr = 4959 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4485 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3920 ## 475 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 12053 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5768254E-10 2.1688676E-10 midg,1,midg; midg,igrid,midg 8.5388080E-10 2.6709017E-11 1,midg,midg; igrid,midg,midg 5.6376065E-10 3.3330547E-10 gauss-seidel spectral radius is 0.9831668 estimated iterations to convergence 63 setup time was (sec) 0.5100000 now iterating at: 16:20:58 rms-change max change #iterations 9.7079061E-02 13.37034 at 10iterations 7.2874008E-03 1.080932 at 20iterations 1.2207675E-03 0.2249680 at 30iterations 4.8379967E-04 7.8605652E-02 at 40iterations 2.1620418E-04 2.9865265E-02 at 50iterations finished qdiffx linear iterations at : 16:21:01 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 2.1620418E-04 2.9865265E-02 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 16:21:02 3.583u 0.160s 0:04.02 93.0% 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 Mon Oct 10 2011 at 16:21:02 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 = 4641 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: 1.654454 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): -63.08400 -7.478000 ymin,ymax (A): -34.76000 29.79300 zmin,zma (A): -29.23600 33.33700 x,y,z range (A): 55.60600 64.55300 62.57300 scale (grids/A): 1.654454 object centre (A): -35.28100 -2.483501 2.050499 number of atom coordinates read : 4641 total number of charged atoms : 4483 net assigned charge : 6.000029 assigned positive charge : 696.0182 centred at (gu) : 91.05769 90.52367 86.20000 assigned negative charge : -690.0222 centred at (gu) : 91.09525 90.62724 86.24113 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 102333 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38638 grid for indexing accessible points = 1.400000 m= 33103 mr = 72709 m= 3642 mr = 23154 m= 118 mr = 1859 m= 0 mr = 25 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 608 time to turn everything in is 0.4800000 number of dielectric boundary points 41449 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 433 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 34477 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) : 0.5514848 object centre at (A) : -35.28100 -2.483501 2.050499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4138268E-02 -5.4274607E-03 midg,1,midg; midg,igrid,midg 6.3437489E-03 1.5097741E-02 1,midg,midg; igrid,midg,midg 6.6906135E-03 2.7695906E-03 gauss-seidel spectral radius is 0.9983983 estimated iterations to convergence 198 setup time was (sec) 0.7000000 now iterating at: 16:21:03 rms-change max change #iterations 4.379448 181.1145 at 10iterations 1.925918 63.71469 at 20iterations 0.8471330 25.29442 at 30iterations 0.3727413 10.63577 at 40iterations 0.1642732 4.667646 at 50iterations 7.2317362E-02 2.182299 at 60iterations 3.2059234E-02 0.9205723 at 70iterations 1.4190325E-02 0.4172831 at 80iterations 6.3849916E-03 0.1869698 at 90iterations 2.9819612E-03 8.7619781E-02 at 100iterations 1.4835221E-03 4.5429230E-02 at 110iterations 8.3745259E-04 2.5089264E-02 at 120iterations finished qdiffx linear iterations at : 16:21:10 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 8.3745259E-04 2.5089264E-02 energy calculations done at 7.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 16:21:10 8.120u 0.223s 0:08.74 95.4% 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 Mon Oct 10 2011 at 16:21:10 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 = 4641 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: 2.481682 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): -63.08400 -7.478000 ymin,ymax (A): -34.76000 29.79300 zmin,zma (A): -29.23600 33.33700 x,y,z range (A): 55.60600 64.55300 62.57300 scale (grids/A): 2.481682 object centre (A): -35.28100 -2.483501 2.050499 number of atom coordinates read : 4641 total number of charged atoms : 4483 net assigned charge : 6.000029 assigned positive charge : 696.0182 centred at (gu) : 91.58629 90.78524 84.29945 assigned negative charge : -690.0222 centred at (gu) : 91.64283 90.94071 84.36146 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 238171 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38638 grid for indexing accessible points = 1.400000 m= 114361 mr = 177825 m= 33570 mr = 91560 m= 5779 mr = 25378 m= 501 mr = 3890 m= 21 mr = 247 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 2247 time to turn everything in is 1.230000 number of dielectric boundary points 93503 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 35820 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) : 1.654454 object centre at (A) : -35.28100 -2.483501 2.050499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3410635 -0.1445434 midg,1,midg; midg,igrid,midg 2.8405331E-02 0.3302844 1,midg,midg; igrid,midg,midg 0.1179850 4.1690100E-02 gauss-seidel spectral radius is 0.9992403 estimated iterations to convergence 286 setup time was (sec) 1.470000 now iterating at: 16:21:12 rms-change max change #iterations 11.38124 289.3495 at 10iterations 6.751234 140.8722 at 20iterations 3.955192 91.24864 at 30iterations 2.315001 52.92595 at 40iterations 1.348544 29.83992 at 50iterations 0.7824795 15.53066 at 60iterations 0.4522681 7.745670 at 70iterations 0.2615533 4.552063 at 80iterations 0.1505653 3.112742 at 90iterations 8.6671032E-02 1.469986 at 100iterations 4.9855173E-02 0.8633552 at 110iterations 2.8603373E-02 0.4941139 at 120iterations 1.6445674E-02 0.2879868 at 130iterations 9.4396593E-03 0.1664152 at 140iterations 5.4327594E-03 8.7613583E-02 at 150iterations 3.1466370E-03 5.9018612E-02 at 160iterations 1.8397871E-03 2.9655457E-02 at 170iterations 1.1002354E-03 1.8367767E-02 at 180iterations finished qdiffx linear iterations at : 16:21:24 total time elapsed so far: 13.30000 # loops : 180 mean,max change (kT/e) : 1.1002354E-03 1.8367767E-02 energy calculations done at 13.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.45000 DelPhi exited at 16:21:24 13.454u 0.212s 0:13.96 97.8% 0+0k 0+0io 0pf+0w