Mon Oct 10 13:59:37 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 13:59:37 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3718 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5350487 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): 9.0000033E-02 66.62600 ymin,ymax (A): -8.342000 38.86100 zmin,zma (A): -19.88100 41.07800 x,y,z range (A): 66.53600 47.20300 60.95900 scale (grids/A): 0.5350487 object centre (A): 33.35800 15.25950 10.59850 number of atom coordinates read : 3718 total number of charged atoms : 3558 net assigned charge : -10.99995 assigned positive charge : 551.3859 centred at (gu) : 88.43385 89.77267 91.13497 assigned negative charge : -562.3875 centred at (gu) : 88.44642 89.80963 91.20977 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6750 nv = 96 ne = 84 npr = 78701 no. pairs analyzed = 78701 no. exposed pairs = 4282 no. arc points = 28797 no. surface atoms = 1467 nbur = 2251 mkacc time = 0.1900000 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= 237 mr = 3756 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.4200000 number of dielectric boundary points 3220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2929 ## 336 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8973 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5713577E-11 -1.1364230E-09 midg,1,midg; midg,igrid,midg -2.4710592E-10 -6.0664002E-10 1,midg,midg; igrid,midg,midg -5.3968519E-10 -3.4561196E-10 gauss-seidel spectral radius is 0.9820444 estimated iterations to convergence 62 setup time was (sec) 0.6700000 now iterating at: 13:59:38 rms-change max change #iterations 7.5049609E-02 11.41918 at 10iterations 5.4038437E-03 0.8299818 at 20iterations 7.8256510E-04 0.1208525 at 30iterations 2.1452717E-04 3.7441254E-02 at 40iterations 6.4317377E-05 1.1379242E-02 at 50iterations finished qdiffx linear iterations at : 13:59:41 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 6.4317377E-05 1.1379242E-02 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 13:59:42 3.645u 0.184s 0:04.28 89.2% 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 13:59:42 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3718 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: 1.605146 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): 9.0000033E-02 66.62600 ymin,ymax (A): -8.342000 38.86100 zmin,zma (A): -19.88100 41.07800 x,y,z range (A): 66.53600 47.20300 60.95900 scale (grids/A): 1.605146 object centre (A): 33.35800 15.25950 10.59850 number of atom coordinates read : 3718 total number of charged atoms : 3558 net assigned charge : -10.99995 assigned positive charge : 551.3859 centred at (gu) : 85.30082 89.31721 93.40394 assigned negative charge : -562.3875 centred at (gu) : 85.33875 89.42834 93.62875 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 76223 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28797 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 23433 mr = 54609 m= 2422 mr = 16484 m= 55 mr = 1281 m= 0 mr = 4 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1565 time to turn everything in is 0.5700000 number of dielectric boundary points 29755 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 291 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 27126 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) : 0.5350487 object centre at (A) : 33.35800 15.25950 10.59850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1364531E-03 -2.7893146E-02 midg,1,midg; midg,igrid,midg -1.1634461E-02 -1.1858743E-02 1,midg,midg; igrid,midg,midg 1.2512873E-03 -6.2495759E-03 gauss-seidel spectral radius is 0.9981781 estimated iterations to convergence 186 setup time was (sec) 0.8700000 now iterating at: 13:59:43 rms-change max change #iterations 3.607718 159.4751 at 10iterations 1.502081 61.51437 at 20iterations 0.6252069 19.98701 at 30iterations 0.2616825 8.561943 at 40iterations 0.1089426 3.670763 at 50iterations 4.5640573E-02 1.473170 at 60iterations 1.9087736E-02 0.6177502 at 70iterations 8.0823600E-03 0.2582617 at 80iterations 3.4868771E-03 0.1175861 at 90iterations 1.5633039E-03 5.6251526E-02 at 100iterations 7.5967092E-04 2.9326886E-02 at 110iterations 4.0769015E-04 1.5426636E-02 at 120iterations finished qdiffx linear iterations at : 13:59:50 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 4.0769015E-04 1.5426636E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.070000 DelPhi exited at 13:59:51 8.074u 0.229s 0:08.66 95.7% 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 13:59:51 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3718 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.407719 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): 9.0000033E-02 66.62600 ymin,ymax (A): -8.342000 38.86100 zmin,zma (A): -19.88100 41.07800 x,y,z range (A): 66.53600 47.20300 60.95900 scale (grids/A): 2.407719 object centre (A): 33.35800 15.25950 10.59850 number of atom coordinates read : 3718 total number of charged atoms : 3558 net assigned charge : -10.99995 assigned positive charge : 551.3859 centred at (gu) : 82.95097 88.97556 95.10566 assigned negative charge : -562.3875 centred at (gu) : 83.00797 89.14236 95.44312 start vw surface at 0.2000000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 177556 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28797 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 82877 mr = 133239 m= 22657 mr = 66841 m= 3885 mr = 17206 m= 238 mr = 2690 m= 3 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 5435 time to turn everything in is 1.420000 number of dielectric boundary points 67127 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 28415 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) : 1.605146 object centre at (A) : 33.35800 15.25950 10.59850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3516481 -0.4300420 midg,1,midg; midg,igrid,midg -0.1907121 -0.1663731 1,midg,midg; igrid,midg,midg 7.8026995E-02 -0.1938976 gauss-seidel spectral radius is 0.9991443 estimated iterations to convergence 270 setup time was (sec) 1.760000 now iterating at: 13:59:53 rms-change max change #iterations 9.454892 345.4326 at 10iterations 5.302232 127.7355 at 20iterations 2.966204 86.83324 at 30iterations 1.654881 35.77568 at 40iterations 0.9191828 18.74268 at 50iterations 0.5101557 10.17577 at 60iterations 0.2822895 5.385178 at 70iterations 0.1560469 3.084679 at 80iterations 8.6131237E-02 1.573639 at 90iterations 4.7598813E-02 0.9090228 at 100iterations 2.6316499E-02 0.4984288 at 110iterations 1.4572792E-02 0.2935715 at 120iterations 8.0882926E-03 0.1671848 at 130iterations 4.5108413E-03 8.4800720E-02 at 140iterations 2.5305410E-03 4.9408913E-02 at 150iterations 1.4562437E-03 2.7980804E-02 at 160iterations 8.6112373E-04 1.8909454E-02 at 170iterations 5.3066586E-04 1.1245728E-02 at 180iterations finished qdiffx linear iterations at : 14:00:04 total time elapsed so far: 13.24000 # loops : 180 mean,max change (kT/e) : 5.3066586E-04 1.1245728E-02 energy calculations done at 13.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.45000 DelPhi exited at 14:00:07 13.449u 0.256s 0:15.90 86.1% 0+0k 0+0io 0pf+0w