Mon Oct 10 11:09:46 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 Mon Oct 10 2011 at 11:09:46 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 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: 0.7468479 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): -21.38100 24.44500 ymin,ymax (A): -7.890000 38.45600 zmin,zma (A): -3.395000 44.27200 x,y,z range (A): 45.82600 46.34600 47.66700 scale (grids/A): 0.7468479 object centre (A): 1.532000 15.28300 20.43850 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.9439 centred at (gu) : 89.04097 89.68237 90.12764 assigned negative charge : -324.9440 centred at (gu) : 89.11649 89.71239 90.34057 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8230 nv = 96 ne = 84 npr = 43922 no. pairs analyzed = 43922 no. exposed pairs = 2724 no. arc points = 19379 no. surface atoms = 919 nbur = 1209 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 565 mr = 4576 m= 5 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.1800000 number of dielectric boundary points 4109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1575 ## 125 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8638 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4103374E-07 -3.6840490E-07 midg,1,midg; midg,igrid,midg -7.0739858E-08 -1.3032658E-07 1,midg,midg; igrid,midg,midg -1.4978934E-08 -1.6147165E-07 gauss-seidel spectral radius is 0.9906600 estimated iterations to convergence 84 setup time was (sec) 0.3700000 now iterating at: 11:09:47 rms-change max change #iterations 0.2520816 34.70712 at 10iterations 3.4749590E-02 4.040682 at 20iterations 4.6843537E-03 0.5923843 at 30iterations 6.5122667E-04 8.1127167E-02 at 40iterations 8.9811285E-05 1.0692596E-02 at 50iterations finished qdiffx linear iterations at : 11:09:49 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 8.9811285E-05 1.0692596E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 11:09:50 3.354u 0.166s 0:03.87 90.6% 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 Mon Oct 10 2011 at 11:09:50 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 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: 2.240544 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): -21.38100 24.44500 ymin,ymax (A): -7.890000 38.45600 zmin,zma (A): -3.395000 44.27200 x,y,z range (A): 45.82600 46.34600 47.66700 scale (grids/A): 2.240544 object centre (A): 1.532000 15.28300 20.43850 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.9439 centred at (gu) : 87.12265 89.04713 90.38297 assigned negative charge : -324.9440 centred at (gu) : 87.34925 89.13712 91.02149 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 86150 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19379 grid for indexing accessible points = 1.400000 m= 34448 mr = 59206 m= 7454 mr = 26206 m= 822 mr = 5267 m= 26 mr = 470 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 868 time to turn everything in is 0.4400000 number of dielectric boundary points 37750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 15853 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) : 0.7468479 object centre at (A) : 1.532000 15.28300 20.43850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7929899E-03 -0.1488691 midg,1,midg; midg,igrid,midg -3.3108007E-02 -1.8845845E-02 1,midg,midg; igrid,midg,midg 6.5612681E-03 -5.5633979E-03 gauss-seidel spectral radius is 0.9989452 estimated iterations to convergence 244 setup time was (sec) 0.6500000 now iterating at: 11:09:51 rms-change max change #iterations 5.200852 213.9603 at 10iterations 2.643223 90.21486 at 20iterations 1.355636 43.07712 at 30iterations 0.6963763 20.75840 at 40iterations 0.3569939 10.08567 at 50iterations 0.1832384 4.821428 at 60iterations 9.4005406E-02 2.873193 at 70iterations 4.8050176E-02 1.441350 at 80iterations 2.4675477E-02 0.7072883 at 90iterations 1.2654602E-02 0.3526874 at 100iterations 6.4698886E-03 0.1884270 at 110iterations 3.3282365E-03 8.8401794E-02 at 120iterations finished qdiffx linear iterations at : 11:09:58 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 3.3282365E-03 8.8401794E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 11:09:58 7.878u 0.196s 0:08.34 96.6% 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 Mon Oct 10 2011 at 11:09:58 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 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: 3.360816 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): -21.38100 24.44500 ymin,ymax (A): -7.890000 38.45600 zmin,zma (A): -3.395000 44.27200 x,y,z range (A): 45.82600 46.34600 47.66700 scale (grids/A): 3.360816 object centre (A): 1.532000 15.28300 20.43850 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.9439 centred at (gu) : 85.68393 88.57051 90.57451 assigned negative charge : -324.9440 centred at (gu) : 86.02389 88.70567 91.53224 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 198190 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19379 grid for indexing accessible points = 1.400000 m= 105371 mr = 142529 m= 45459 mr = 87203 m= 14267 mr = 37817 m= 3413 mr = 11544 m= 441 mr = 2623 m= 19 mr = 302 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 2741 time to turn everything in is 1.330000 number of dielectric boundary points 85142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 15912 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) : 2.240544 object centre at (A) : 1.532000 15.28300 20.43850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0951475E-02 -1.325583 midg,1,midg; midg,igrid,midg -0.3201404 -0.1109582 1,midg,midg; igrid,midg,midg 8.3516039E-02 -0.1524979 gauss-seidel spectral radius is 0.9993250 estimated iterations to convergence 304 setup time was (sec) 1.570000 now iterating at: 11:10:00 rms-change max change #iterations 11.19304 300.4802 at 10iterations 6.612760 136.6751 at 20iterations 3.920319 76.47090 at 30iterations 2.314109 43.43831 at 40iterations 1.365789 28.02203 at 50iterations 0.8054510 13.35580 at 60iterations 0.4750796 7.385718 at 70iterations 0.2802827 5.022747 at 80iterations 0.1650517 2.616690 at 90iterations 9.7293660E-02 1.545696 at 100iterations 5.7116188E-02 0.9241095 at 110iterations 3.3668201E-02 0.5437965 at 120iterations 1.9809505E-02 0.3140855 at 130iterations 1.1676138E-02 0.1836357 at 140iterations 6.8725515E-03 0.1150284 at 150iterations 4.0458143E-03 6.6940308E-02 at 160iterations 2.3857867E-03 3.5237312E-02 at 170iterations 1.4041853E-03 2.1844864E-02 at 180iterations finished qdiffx linear iterations at : 11:10:12 total time elapsed so far: 12.99000 # loops : 180 mean,max change (kT/e) : 1.4041853E-03 2.1844864E-02 energy calculations done at 12.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.13000 DelPhi exited at 11:10:12 13.128u 0.204s 0:13.60 97.9% 0+0k 0+0io 0pf+0w