Mon Oct 10 19:34:19 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 19:34:19 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 = 2776 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: 0.5773410 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): 1.317000 62.97900 ymin,ymax (A): 12.17400 58.86300 zmin,zma (A): -7.240000 40.34100 x,y,z range (A): 61.66200 46.68900 47.58101 scale (grids/A): 0.5773410 object centre (A): 32.14800 35.51850 16.55050 number of atom coordinates read : 2776 total number of charged atoms : 2637 net assigned charge : -3.499968 assigned positive charge : 413.1753 centred at (gu) : 89.40936 89.63708 89.53190 assigned negative charge : -416.6764 centred at (gu) : 89.39198 89.79526 89.45882 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6011 nv = 96 ne = 84 npr = 56090 no. pairs analyzed = 56090 no. exposed pairs = 3654 no. arc points = 25763 no. surface atoms = 1230 nbur = 1546 mkacc time = 9.0000004E-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 = 1.512000 m= 259 mr = 3033 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2596 ## 280 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7741 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3333910E-09 5.9745225E-10 midg,1,midg; midg,igrid,midg 2.4418376E-09 -3.4333616E-09 1,midg,midg; igrid,midg,midg -1.1761256E-09 -3.2476352E-10 gauss-seidel spectral radius is 0.9845019 estimated iterations to convergence 66 setup time was (sec) 0.4100000 now iterating at: 19:34:20 rms-change max change #iterations 8.9585930E-02 13.11100 at 10iterations 6.8041007E-03 1.100066 at 20iterations 5.2304199E-04 0.1087580 at 30iterations 4.1716528E-05 6.3133240E-03 at 40iterations 3.2708595E-06 5.5122375E-04 at 50iterations finished qdiffx linear iterations at : 19:34:23 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 3.2708595E-06 5.5122375E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 19:34:23 3.431u 0.155s 0:04.29 83.4% 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 19:34:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2776 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: 1.732023 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): 1.317000 62.97900 ymin,ymax (A): 12.17400 58.86300 zmin,zma (A): -7.240000 40.34100 x,y,z range (A): 61.66200 46.68900 47.58101 scale (grids/A): 1.732023 object centre (A): 32.14800 35.51850 16.55050 number of atom coordinates read : 2776 total number of charged atoms : 2637 net assigned charge : -3.499968 assigned positive charge : 413.1753 centred at (gu) : 88.22712 88.91065 88.59507 assigned negative charge : -416.6764 centred at (gu) : 88.17559 89.38545 88.37624 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 66547 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25763 grid for indexing accessible points = 1.400000 m= 20343 mr = 44560 m= 2205 mr = 13876 m= 59 mr = 1026 m= 0 mr = 4 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 888 time to turn everything in is 0.3200000 number of dielectric boundary points 29688 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 263 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 20455 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) : 0.5773410 object centre at (A) : 32.14800 35.51850 16.55050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.7117680E-03 -4.2255019E-04 midg,1,midg; midg,igrid,midg 1.2455003E-02 -2.0737909E-02 1,midg,midg; igrid,midg,midg -3.2353210E-03 -1.5755657E-02 gauss-seidel spectral radius is 0.9983734 estimated iterations to convergence 197 setup time was (sec) 0.5300000 now iterating at: 19:34:24 rms-change max change #iterations 3.582598 155.7075 at 10iterations 1.558021 57.05681 at 20iterations 0.6792752 25.05769 at 30iterations 0.2958022 10.52779 at 40iterations 0.1288447 5.042206 at 50iterations 5.6245364E-02 2.103010 at 60iterations 2.4653004E-02 0.8772397 at 70iterations 1.0720793E-02 0.3753014 at 80iterations 4.6900604E-03 0.1695232 at 90iterations 2.0523982E-03 7.1744919E-02 at 100iterations 8.9586491E-04 3.0132294E-02 at 110iterations 3.9050227E-04 1.2336731E-02 at 120iterations finished qdiffx linear iterations at : 19:34:31 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 3.9050227E-04 1.2336731E-02 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 19:34:32 7.599u 0.207s 0:08.57 90.8% 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 19:34:32 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 = 2776 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: 2.598034 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): 1.317000 62.97900 ymin,ymax (A): 12.17400 58.86300 zmin,zma (A): -7.240000 40.34100 x,y,z range (A): 61.66200 46.68900 47.58101 scale (grids/A): 2.598034 object centre (A): 32.14800 35.51850 16.55050 number of atom coordinates read : 2776 total number of charged atoms : 2637 net assigned charge : -3.499968 assigned positive charge : 413.1753 centred at (gu) : 87.34048 88.36575 87.89229 assigned negative charge : -416.6764 centred at (gu) : 87.26324 89.07819 87.56444 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 154277 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25763 grid for indexing accessible points = 1.400000 m= 70161 mr = 108773 m= 20236 mr = 55185 m= 3351 mr = 15080 m= 252 mr = 2123 m= 7 mr = 101 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 3039 time to turn everything in is 0.8000000 number of dielectric boundary points 67023 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 21091 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) : 1.732023 object centre at (A) : 32.14800 35.51850 16.55050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.3348343E-02 -1.0623477E-02 midg,1,midg; midg,igrid,midg 0.1940092 -0.2417930 1,midg,midg; igrid,midg,midg 3.6295433E-02 -0.2445260 gauss-seidel spectral radius is 0.9991961 estimated iterations to convergence 278 setup time was (sec) 1.030000 now iterating at: 19:34:33 rms-change max change #iterations 9.059835 283.0352 at 10iterations 5.187391 144.9070 at 20iterations 2.944001 67.45778 at 30iterations 1.667366 43.95931 at 40iterations 0.9434081 21.66166 at 50iterations 0.5326181 11.24539 at 60iterations 0.2989522 6.373662 at 70iterations 0.1685423 3.397020 at 80iterations 9.4677918E-02 1.928658 at 90iterations 5.3128995E-02 1.141712 at 100iterations 2.9838171E-02 0.6196995 at 110iterations 1.6737962E-02 0.3373432 at 120iterations 9.3950555E-03 0.2045898 at 130iterations 5.2588806E-03 0.1044350 at 140iterations 2.9504071E-03 6.0617447E-02 at 150iterations 1.6580384E-03 3.2302856E-02 at 160iterations 9.2731579E-04 1.8220901E-02 at 170iterations 5.2053994E-04 1.0584354E-02 at 180iterations finished qdiffx linear iterations at : 19:34:45 total time elapsed so far: 12.25000 # loops : 180 mean,max change (kT/e) : 5.2053994E-04 1.0584354E-02 energy calculations done at 12.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.38000 DelPhi exited at 19:34:45 12.386u 0.209s 0:12.98 96.9% 0+0k 0+0io 0pf+0w