Tue Oct 11 03:20:25 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+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 Tue Oct 11 2011 at 03:20:25 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3158 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5368479 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): -6.5000057E-02 46.31700 ymin,ymax (A): 70.95000 137.2630 zmin,zma (A): 102.3240 161.6830 x,y,z range (A): 46.38200 66.31300 59.35900 scale (grids/A): 0.5368479 object centre (A): 23.12600 104.1065 132.0035 number of atom coordinates read : 3158 total number of charged atoms : 3019 net assigned charge : -5.999976 assigned positive charge : 471.6838 centred at (gu) : 90.38935 92.84252 91.52430 assigned negative charge : -477.6848 centred at (gu) : 90.34277 92.87181 91.52356 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5720 nv = 96 ne = 84 npr = 65729 no. pairs analyzed = 65729 no. exposed pairs = 3821 no. arc points = 26204 no. surface atoms = 1298 nbur = 1860 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 = 1.596000 m= 204 mr = 3051 m= 0 mr = 11 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 2862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2716 ## 409 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7684 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7731550E-10 -3.6205869E-10 midg,1,midg; midg,igrid,midg -5.6733739E-11 -8.1748108E-10 1,midg,midg; igrid,midg,midg -4.4083248E-10 -2.3383540E-11 gauss-seidel spectral radius is 0.9821239 estimated iterations to convergence 62 setup time was (sec) 0.6500000 now iterating at: 03:20:26 rms-change max change #iterations 7.1985655E-02 10.34386 at 10iterations 4.7738003E-03 0.7952307 at 20iterations 3.6219083E-04 6.8120003E-02 at 30iterations 5.0472412E-05 9.9922419E-03 at 40iterations 1.0562610E-05 2.2568703E-03 at 50iterations finished qdiffx linear iterations at : 03:20:30 total time elapsed so far: 4.950000 # loops : 50 mean,max change (kT/e) : 1.0562610E-05 2.2568703E-03 energy calculations done at 4.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.130000 DelPhi exited at 03:20:31 5.134u 0.445s 0:05.99 92.9% 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 Tue Oct 11 2011 at 03:20:31 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3158 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.610544 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): -6.5000057E-02 46.31700 ymin,ymax (A): 70.95000 137.2630 zmin,zma (A): 102.3240 161.6830 x,y,z range (A): 46.38200 66.31300 59.35900 scale (grids/A): 1.610544 object centre (A): 23.12600 104.1065 132.0035 number of atom coordinates read : 3158 total number of charged atoms : 3019 net assigned charge : -5.999976 assigned positive charge : 471.6838 centred at (gu) : 91.16724 98.52670 94.57195 assigned negative charge : -477.6848 centred at (gu) : 91.02805 98.61488 94.57018 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 63725 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26204 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 19168 mr = 43772 m= 1895 mr = 13331 m= 36 mr = 925 m= 0 mr = 2 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 339 time to turn everything in is 0.5600000 number of dielectric boundary points 26794 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 374 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 23006 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) : 0.5368479 object centre at (A) : 23.12600 104.1065 132.0035 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8930646E-03 3.1494719E-03 midg,1,midg; midg,igrid,midg 2.2547057E-02 -6.5590930E-03 1,midg,midg; igrid,midg,midg -9.5331213E-03 -3.6829545E-03 gauss-seidel spectral radius is 0.9981335 estimated iterations to convergence 184 setup time was (sec) 0.9400000 now iterating at: 03:20:32 rms-change max change #iterations 3.321444 143.5441 at 10iterations 1.363606 50.95011 at 20iterations 0.5631432 19.53182 at 30iterations 0.2326270 8.222935 at 40iterations 9.5627204E-02 3.700415 at 50iterations 3.9565053E-02 1.476830 at 60iterations 1.6336914E-02 0.5956542 at 70iterations 6.7389491E-03 0.2485543 at 80iterations 2.8086691E-03 0.1109657 at 90iterations 1.1670025E-03 4.6470642E-02 at 100iterations 4.9284229E-04 2.0334244E-02 at 110iterations 2.1347401E-04 9.0593100E-03 at 120iterations finished qdiffx linear iterations at : 03:20:43 total time elapsed so far: 11.80000 # loops : 120 mean,max change (kT/e) : 2.1347401E-04 9.0593100E-03 energy calculations done at 11.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.99000 DelPhi exited at 03:20:44 11.995u 0.514s 0:12.98 96.3% 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 Tue Oct 11 2011 at 03:20:44 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3158 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.415816 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): -6.5000057E-02 46.31700 ymin,ymax (A): 70.95000 137.2630 zmin,zma (A): 102.3240 161.6830 x,y,z range (A): 46.38200 66.31300 59.35900 scale (grids/A): 2.415816 object centre (A): 23.12600 104.1065 132.0035 number of atom coordinates read : 3158 total number of charged atoms : 3019 net assigned charge : -5.999976 assigned positive charge : 471.6838 centred at (gu) : 91.75073 102.7898 96.85779 assigned negative charge : -477.6848 centred at (gu) : 91.54187 102.9221 96.85514 start vw surface at 0.1300000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 148368 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26204 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 67355 mr = 107247 m= 18294 mr = 53510 m= 2924 mr = 13818 m= 177 mr = 1893 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 1065 time to turn everything in is 1.340000 number of dielectric boundary points 60593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 24114 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) : 1.610544 object centre at (A) : 23.12600 104.1065 132.0035 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5881866E-02 0.1431456 midg,1,midg; midg,igrid,midg 0.4075980 -0.2866032 1,midg,midg; igrid,midg,midg -0.1555085 -4.6748552E-02 gauss-seidel spectral radius is 0.9991205 estimated iterations to convergence 266 setup time was (sec) 1.690000 now iterating at: 03:20:46 rms-change max change #iterations 8.654688 277.9650 at 10iterations 4.830009 121.9245 at 20iterations 2.679211 61.91451 at 30iterations 1.481281 34.80693 at 40iterations 0.8148169 18.88236 at 50iterations 0.4486221 9.637625 at 60iterations 0.2466831 5.071767 at 70iterations 0.1350605 2.840134 at 80iterations 7.4042112E-02 1.827032 at 90iterations 4.0500570E-02 0.9145483 at 100iterations 2.2137711E-02 0.4546013 at 110iterations 1.2113755E-02 0.2527313 at 120iterations 6.6382224E-03 0.1339082 at 130iterations 3.6210094E-03 7.0970535E-02 at 140iterations 1.9782896E-03 4.2201996E-02 at 150iterations 1.0803652E-03 2.4448395E-02 at 160iterations 5.9032597E-04 1.1919022E-02 at 170iterations 3.2255196E-04 6.8063736E-03 at 180iterations finished qdiffx linear iterations at : 03:21:04 total time elapsed so far: 19.60000 # loops : 180 mean,max change (kT/e) : 3.2255196E-04 6.8063736E-03 energy calculations done at 19.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.76000 DelPhi exited at 03:21:05 19.765u 0.539s 0:20.66 98.2% 0+0k 0+0io 0pf+0w