Sat Oct 15 13:37:25 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 15 2011 at 13:37:25 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2099 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7446453 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): -23.67800 24.13000 ymin,ymax (A): 7.379000 53.37900 zmin,zma (A): -3.119000 43.92100 x,y,z range (A): 47.80800 46.00000 47.04000 scale (grids/A): 0.7446453 object centre (A): 0.2259998 30.37900 20.40100 number of atom coordinates read : 2099 total number of charged atoms : 1961 net assigned charge : -4.999990 assigned positive charge : 314.1920 centred at (gu) : 90.34362 89.65026 89.93594 assigned negative charge : -319.1920 centred at (gu) : 90.35354 89.62674 90.09759 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8045 nv = 96 ne = 84 npr = 43243 no. pairs analyzed = 43243 no. exposed pairs = 2667 no. arc points = 18634 no. surface atoms = 903 nbur = 1196 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 592 mr = 4513 m= 2 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 74 time to turn everything in is 0.1800000 number of dielectric boundary points 4013 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1596 ## 127 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8449 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.1078063E-08 -2.7670970E-07 midg,1,midg; midg,igrid,midg -1.3159797E-07 -6.6896028E-08 1,midg,midg; igrid,midg,midg -8.1110407E-08 -1.1522131E-07 gauss-seidel spectral radius is 0.9905997 estimated iterations to convergence 84 setup time was (sec) 0.4100000 now iterating at: 13:37:27 rms-change max change #iterations 0.2468981 33.83059 at 10iterations 3.4167506E-02 4.399975 at 20iterations 4.6535712E-03 0.5754642 at 30iterations 6.3132733E-04 9.1269016E-02 at 40iterations 8.5249769E-05 1.1692047E-02 at 50iterations finished qdiffx linear iterations at : 13:37:32 total time elapsed so far: 3.810000 # loops : 50 mean,max change (kT/e) : 8.5249769E-05 1.1692047E-02 energy calculations done at 3.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.950000 DelPhi exited at 13:37:33 3.950u 0.250s 0:07.36 57.0% 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 15 2011 at 13:37:33 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2099 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.233936 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): -23.67800 24.13000 ymin,ymax (A): 7.379000 53.37900 zmin,zma (A): -3.119000 43.92100 x,y,z range (A): 47.80800 46.00000 47.04000 scale (grids/A): 2.233936 object centre (A): 0.2259998 30.37900 20.40100 number of atom coordinates read : 2099 total number of charged atoms : 1961 net assigned charge : -4.999990 assigned positive charge : 314.1920 centred at (gu) : 91.03061 88.95074 89.80772 assigned negative charge : -319.1920 centred at (gu) : 91.06068 88.88019 90.29277 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 84399 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18634 grid for indexing accessible points = 1.400000 m= 33800 mr = 58510 m= 7087 mr = 25685 m= 736 mr = 4910 m= 22 mr = 414 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1913 time to turn everything in is 0.4500000 number of dielectric boundary points 36526 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 38 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 15626 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) : 0.7446453 object centre at (A) : 0.2259998 30.37900 20.40100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7916081E-03 -0.1200063 midg,1,midg; midg,igrid,midg -3.7235767E-02 -3.3236913E-02 1,midg,midg; igrid,midg,midg 1.0659156E-02 9.1243666E-03 gauss-seidel spectral radius is 0.9989370 estimated iterations to convergence 243 setup time was (sec) 0.7300000 now iterating at: 13:37:34 rms-change max change #iterations 5.102783 206.2684 at 10iterations 2.593225 83.75074 at 20iterations 1.325886 37.67464 at 30iterations 0.6779932 20.11730 at 40iterations 0.3467421 10.21639 at 50iterations 0.1777293 4.641490 at 60iterations 9.0953372E-02 2.547664 at 70iterations 4.6515223E-02 1.323301 at 80iterations 2.3816902E-02 0.6475052 at 90iterations 1.2176656E-02 0.3305054 at 100iterations 6.2445588E-03 0.1686926 at 110iterations 3.1860131E-03 9.9506855E-02 at 120iterations finished qdiffx linear iterations at : 13:37:48 total time elapsed so far: 8.660000 # loops : 120 mean,max change (kT/e) : 3.1860131E-03 9.9506855E-02 energy calculations done at 8.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.790000 DelPhi exited at 13:37:48 8.797u 0.369s 0:15.58 58.7% 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 15 2011 at 13:37:52 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2099 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.350904 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): -23.67800 24.13000 ymin,ymax (A): 7.379000 53.37900 zmin,zma (A): -3.119000 43.92100 x,y,z range (A): 47.80800 46.00000 47.04000 scale (grids/A): 3.350904 object centre (A): 0.2259998 30.37900 20.40100 number of atom coordinates read : 2099 total number of charged atoms : 1961 net assigned charge : -4.999990 assigned positive charge : 314.1920 centred at (gu) : 91.54576 88.42620 89.71172 assigned negative charge : -319.1920 centred at (gu) : 91.59103 88.32030 90.43909 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 193928 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18634 grid for indexing accessible points = 1.400000 m= 103343 mr = 140418 m= 44299 mr = 85736 m= 13576 mr = 36814 m= 3019 mr = 10766 m= 367 mr = 2301 m= 12 mr = 233 m= 0 mr = 4 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 6143 time to turn everything in is 1.340000 number of dielectric boundary points 82272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 15688 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) : 2.233936 object centre at (A) : 0.2259998 30.37900 20.40100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1174926 -1.202441 midg,1,midg; midg,igrid,midg -0.2066890 -0.2790403 1,midg,midg; igrid,midg,midg -6.6965729E-02 7.9037286E-02 gauss-seidel spectral radius is 0.9993210 estimated iterations to convergence 303 setup time was (sec) 1.610000 now iterating at: 13:37:55 rms-change max change #iterations 11.08213 338.8209 at 10iterations 6.541010 121.1554 at 20iterations 3.871690 76.18336 at 30iterations 2.279255 38.03749 at 40iterations 1.343885 22.98777 at 50iterations 0.7923679 16.93760 at 60iterations 0.4655944 7.833065 at 70iterations 0.2742558 4.360262 at 80iterations 0.1611757 2.638996 at 90iterations 9.4731234E-02 1.581491 at 100iterations 5.5778593E-02 0.8991661 at 110iterations 3.2790877E-02 0.5367889 at 120iterations 1.9292483E-02 0.3048863 at 130iterations 1.1334561E-02 0.1905117 at 140iterations 6.6820411E-03 0.1090720 at 150iterations 3.9132126E-03 6.3333511E-02 at 160iterations 2.3041244E-03 3.8272858E-02 at 170iterations 1.3565669E-03 2.2578716E-02 at 180iterations finished qdiffx linear iterations at : 13:38:13 total time elapsed so far: 15.00000 # loops : 180 mean,max change (kT/e) : 1.3565669E-03 2.2578716E-02 energy calculations done at 15.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.13000 DelPhi exited at 13:38:13 15.136u 0.289s 0:21.67 71.1% 0+0k 0+0io 0pf+0w