Mon Oct 10 17:03:40 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 17:03:40 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3654 !!! WARNING: HIT 104 has a net charge of 0.5140 !!! WARNING: HIR 145 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5281351 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): -16.69600 50.71100 ymin,ymax (A): -27.58000 28.79400 zmin,zma (A): -22.73400 34.93500 x,y,z range (A): 67.40700 56.37400 57.66900 scale (grids/A): 0.5281351 object centre (A): 17.00750 0.6069994 6.100501 number of atom coordinates read : 3654 total number of charged atoms : 3507 net assigned charge : -1.971964 assigned positive charge : 562.5326 centred at (gu) : 89.94520 88.24878 89.57394 assigned negative charge : -564.5067 centred at (gu) : 89.91261 88.10740 89.62899 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6652 nv = 96 ne = 84 npr = 69507 no. pairs analyzed = 69507 no. exposed pairs = 5205 no. arc points = 37470 no. surface atoms = 1731 nbur = 1923 mkacc time = 0.1700000 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 = 1.624000 m= 244 mr = 2990 m= 0 mr = 3 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3903 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3723 ## 545 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8822 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0381331E-10 -2.5276606E-10 midg,1,midg; midg,igrid,midg -1.0358020E-09 3.4175712E-10 1,midg,midg; igrid,midg,midg -1.8882518E-10 8.7258090E-11 gauss-seidel spectral radius is 0.9815972 estimated iterations to convergence 61 setup time was (sec) 0.6400000 now iterating at: 17:03:41 rms-change max change #iterations 6.8316177E-02 12.23403 at 10iterations 4.2199823E-03 0.7388344 at 20iterations 2.5124403E-04 4.0105820E-02 at 30iterations 1.5378520E-05 2.5258064E-03 at 40iterations 9.6933536E-07 1.5640259E-04 at 50iterations finished qdiffx linear iterations at : 17:03:43 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 9.6933536E-07 1.5640259E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 17:03:44 3.438u 0.142s 0:03.94 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 17:03:44 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3654 !!! WARNING: HIT 104 has a net charge of 0.5140 !!! WARNING: HIR 145 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.584405 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): -16.69600 50.71100 ymin,ymax (A): -27.58000 28.79400 zmin,zma (A): -22.73400 34.93500 x,y,z range (A): 67.40700 56.37400 57.66900 scale (grids/A): 1.584405 object centre (A): 17.00750 0.6069994 6.100501 number of atom coordinates read : 3654 total number of charged atoms : 3507 net assigned charge : -1.971964 assigned positive charge : 562.5326 centred at (gu) : 89.83447 84.74490 88.72093 assigned negative charge : -564.5067 centred at (gu) : 89.73761 84.32159 88.88619 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 73350 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37470 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20464 mr = 45992 m= 1862 mr = 12916 m= 34 mr = 680 m= 0 mr = 2 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1144 time to turn everything in is 0.5500000 number of dielectric boundary points 36120 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 543 ## 17 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 26682 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) : 0.5281351 object centre at (A) : 17.00750 0.6069994 6.100501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3441598E-02 -1.7165352E-03 midg,1,midg; midg,igrid,midg -8.2157217E-03 2.8028416E-03 1,midg,midg; igrid,midg,midg -3.0337272E-02 -1.7780777E-02 gauss-seidel spectral radius is 0.9981562 estimated iterations to convergence 185 setup time was (sec) 0.8400000 now iterating at: 17:03:45 rms-change max change #iterations 3.565572 164.9505 at 10iterations 1.467271 63.59082 at 20iterations 0.6014833 21.50700 at 30iterations 0.2480443 8.447371 at 40iterations 0.1026303 3.970329 at 50iterations 4.2390257E-02 1.566221 at 60iterations 1.7509680E-02 0.6348352 at 70iterations 7.2125117E-03 0.2488918 at 80iterations 2.9889990E-03 9.8508835E-02 at 90iterations 1.2375790E-03 5.1824093E-02 at 100iterations 5.1001075E-04 1.7566681E-02 at 110iterations 2.1173859E-04 7.2612762E-03 at 120iterations finished qdiffx linear iterations at : 17:03:51 total time elapsed so far: 7.430000 # loops : 120 mean,max change (kT/e) : 2.1173859E-04 7.2612762E-03 energy calculations done at 7.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 17:03:52 7.622u 0.197s 0:08.57 91.1% 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 17:03:52 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3654 !!! WARNING: HIT 104 has a net charge of 0.5140 !!! WARNING: HIR 145 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.376608 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): -16.69600 50.71100 ymin,ymax (A): -27.58000 28.79400 zmin,zma (A): -22.73400 34.93500 x,y,z range (A): 67.40700 56.37400 57.66900 scale (grids/A): 2.376608 object centre (A): 17.00750 0.6069994 6.100501 number of atom coordinates read : 3654 total number of charged atoms : 3507 net assigned charge : -1.971964 assigned positive charge : 562.5326 centred at (gu) : 89.75141 82.11716 88.08111 assigned negative charge : -564.5067 centred at (gu) : 89.60622 81.48234 88.32922 start vw surface at 0.1700000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 170925 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37470 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 71713 mr = 114395 m= 18439 mr = 53435 m= 2506 mr = 12930 m= 129 mr = 1396 m= 3 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 3524 time to turn everything in is 1.310000 number of dielectric boundary points 81537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 27996 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) : 1.584405 object centre at (A) : 17.00750 0.6069994 6.100501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2389331 -1.0581935E-02 midg,1,midg; midg,igrid,midg -7.5538889E-02 1.1824234E-02 1,midg,midg; igrid,midg,midg -0.6390945 -0.7080252 gauss-seidel spectral radius is 0.9991530 estimated iterations to convergence 271 setup time was (sec) 1.640000 now iterating at: 17:03:54 rms-change max change #iterations 9.530290 262.8078 at 10iterations 5.428194 155.1514 at 20iterations 3.064526 67.29130 at 30iterations 1.716744 37.59904 at 40iterations 0.9604762 21.20660 at 50iterations 0.5354044 11.98548 at 60iterations 0.2973781 6.448478 at 70iterations 0.1651231 3.756714 at 80iterations 9.1550782E-02 1.937956 at 90iterations 5.0631203E-02 0.9864168 at 100iterations 2.8011112E-02 0.6363163 at 110iterations 1.5494294E-02 0.3059196 at 120iterations 8.5632391E-03 0.1735687 at 130iterations 4.7370400E-03 9.2215538E-02 at 140iterations 2.6144192E-03 5.4384232E-02 at 150iterations 1.4410183E-03 2.7040482E-02 at 160iterations 7.9714489E-04 1.5586019E-02 at 170iterations 4.3976441E-04 8.2378387E-03 at 180iterations finished qdiffx linear iterations at : 17:04:09 total time elapsed so far: 15.84000 # loops : 180 mean,max change (kT/e) : 4.3976441E-04 8.2378387E-03 energy calculations done at 15.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.04000 DelPhi exited at 17:04:10 16.046u 0.239s 0:17.85 91.1% 0+0k 0+0io 0pf+0w