Sat Oct 15 13:38:53 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 15 2011 at 13:38:53 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2896 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5802109 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): 16.68700 78.04400 ymin,ymax (A): -43.78500 8.387000 zmin,zma (A): -7.078000 48.16900 x,y,z range (A): 61.35700 52.17200 55.24700 scale (grids/A): 0.5802109 object centre (A): 47.36550 -17.69900 20.54550 number of atom coordinates read : 2896 total number of charged atoms : 2750 net assigned charge : 13.00002 assigned positive charge : 426.8228 centred at (gu) : 90.81081 89.88224 91.75589 assigned negative charge : -413.8235 centred at (gu) : 90.65667 89.88873 91.95409 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6659 nv = 96 ne = 84 npr = 54463 no. pairs analyzed = 54463 no. exposed pairs = 4539 no. arc points = 32975 no. surface atoms = 1489 nbur = 1407 mkacc time = 8.9999996E-02 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 = 1.484000 m= 382 mr = 2834 m= 5 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 4196 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3223 ## 382 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8333 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5907633E-09 -2.0190312E-09 midg,1,midg; midg,igrid,midg 3.1243834E-09 2.7021370E-09 1,midg,midg; igrid,midg,midg -2.3838131E-10 7.2733832E-09 gauss-seidel spectral radius is 0.9846854 estimated iterations to convergence 66 setup time was (sec) 0.4600000 now iterating at: 13:38:54 rms-change max change #iterations 9.6677914E-02 17.61435 at 10iterations 7.3137223E-03 1.148323 at 20iterations 5.8402086E-04 8.1865311E-02 at 30iterations 5.4084157E-05 7.7610016E-03 at 40iterations 7.1820314E-06 9.8991394E-04 at 50iterations finished qdiffx linear iterations at : 13:39:01 total time elapsed so far: 3.700000 # loops : 50 mean,max change (kT/e) : 7.1820314E-06 9.8991394E-04 energy calculations done at 3.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.820000 DelPhi exited at 13:39:02 3.825u 0.258s 0:08.86 45.9% 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 13:39:02 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2896 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.740633 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): 16.68700 78.04400 ymin,ymax (A): -43.78500 8.387000 zmin,zma (A): -7.078000 48.16900 x,y,z range (A): 61.35700 52.17200 55.24700 scale (grids/A): 1.740633 object centre (A): 47.36550 -17.69900 20.54550 number of atom coordinates read : 2896 total number of charged atoms : 2750 net assigned charge : 13.00002 assigned positive charge : 426.8228 centred at (gu) : 92.43180 89.64627 95.26695 assigned negative charge : -413.8235 centred at (gu) : 91.97008 89.66586 95.86214 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70600 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32975 grid for indexing accessible points = 1.400000 m= 23580 mr = 42077 m= 3651 mr = 15095 m= 168 mr = 1876 m= 0 mr = 18 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 38933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 308 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 21351 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) : 0.5802109 object centre at (A) : 47.36550 -17.69900 20.54550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6079813E-02 1.7384253E-02 midg,1,midg; midg,igrid,midg 1.6979527E-02 1.2542416E-02 1,midg,midg; igrid,midg,midg -2.3665812E-02 3.1539716E-02 gauss-seidel spectral radius is 0.9984285 estimated iterations to convergence 200 setup time was (sec) 0.6100000 now iterating at: 13:39:03 rms-change max change #iterations 3.692658 158.7026 at 10iterations 1.618911 55.93785 at 20iterations 0.7155496 30.61682 at 30iterations 0.3135065 11.18076 at 40iterations 0.1384424 4.769861 at 50iterations 6.1273072E-02 2.132957 at 60iterations 2.6937786E-02 1.009403 at 70iterations 1.1928155E-02 0.3995152 at 80iterations 5.2591218E-03 0.1648045 at 90iterations 2.3138339E-03 9.1089249E-02 at 100iterations 1.0274262E-03 3.4975052E-02 at 110iterations 4.5323541E-04 1.6414642E-02 at 120iterations finished qdiffx linear iterations at : 13:39:20 total time elapsed so far: 8.700000 # loops : 120 mean,max change (kT/e) : 4.5323541E-04 1.6414642E-02 energy calculations done at 8.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.840000 DelPhi exited at 13:39:22 8.841u 0.291s 0:19.89 45.9% 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 13:39:23 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2896 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.610949 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): 16.68700 78.04400 ymin,ymax (A): -43.78500 8.387000 zmin,zma (A): -7.078000 48.16900 x,y,z range (A): 61.35700 52.17200 55.24700 scale (grids/A): 2.610949 object centre (A): 47.36550 -17.69900 20.54550 number of atom coordinates read : 2896 total number of charged atoms : 2750 net assigned charge : 13.00002 assigned positive charge : 426.8228 centred at (gu) : 93.64737 89.46936 97.90020 assigned negative charge : -413.8235 centred at (gu) : 92.95499 89.49868 98.79321 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 162646 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32975 grid for indexing accessible points = 1.400000 m= 75251 mr = 104089 m= 26440 mr = 55858 m= 6174 mr = 19104 m= 678 mr = 4005 m= 13 mr = 354 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9600000 number of dielectric boundary points 87792 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 21995 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) : 1.740633 object centre at (A) : 47.36550 -17.69900 20.54550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3569742 0.2514615 midg,1,midg; midg,igrid,midg 0.2108331 0.1575772 1,midg,midg; igrid,midg,midg -0.4960139 0.4289401 gauss-seidel spectral radius is 0.9992307 estimated iterations to convergence 285 setup time was (sec) 1.270000 now iterating at: 13:39:26 rms-change max change #iterations 9.560984 285.8409 at 10iterations 5.695588 157.7235 at 20iterations 3.335348 82.64857 at 30iterations 1.939469 56.19805 at 40iterations 1.121562 33.14317 at 50iterations 0.6452996 15.50691 at 60iterations 0.3721786 8.383230 at 70iterations 0.2129583 4.941971 at 80iterations 0.1216826 2.959825 at 90iterations 6.9529548E-02 1.584221 at 100iterations 3.9665129E-02 0.8732414 at 110iterations 2.2585537E-02 0.4615784 at 120iterations 1.2861974E-02 0.2559652 at 130iterations 7.3235282E-03 0.1630268 at 140iterations 4.1570789E-03 8.5246563E-02 at 150iterations 2.3643470E-03 4.7225952E-02 at 160iterations 1.3454349E-03 2.5884628E-02 at 170iterations 7.6550047E-04 1.7059326E-02 at 180iterations finished qdiffx linear iterations at : 13:39:51 total time elapsed so far: 15.01000 # loops : 180 mean,max change (kT/e) : 7.6550047E-04 1.7059326E-02 energy calculations done at 15.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.14000 DelPhi exited at 13:39:52 15.144u 0.358s 0:28.93 53.5% 0+0k 0+0io 0pf+0w