Mon Oct 10 19:42:45 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 19:42:45 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3055 !!! WARNING: TYR 265 has a net charge of -0.2720 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: 0.5438519 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): -4.114000 61.34500 ymin,ymax (A): 13.54800 69.22000 zmin,zma (A): -13.29300 51.59600 x,y,z range (A): 65.45900 55.67200 64.88900 scale (grids/A): 0.5438519 object centre (A): 28.61550 41.38400 19.15150 number of atom coordinates read : 3055 total number of charged atoms : 2915 net assigned charge : 4.228020 assigned positive charge : 454.6450 centred at (gu) : 91.45697 91.73693 90.66440 assigned negative charge : -450.4183 centred at (gu) : 91.48035 91.70899 90.73771 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6095 nv = 96 ne = 84 npr = 58134 no. pairs analyzed = 58134 no. exposed pairs = 4488 no. arc points = 33157 no. surface atoms = 1486 nbur = 1569 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= 245 mr = 2650 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 0.3800000 number of dielectric boundary points 3687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3310 ## 451 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 7877 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8658223E-10 -2.5522703E-10 midg,1,midg; midg,igrid,midg 4.8483450E-11 6.3886635E-10 1,midg,midg; igrid,midg,midg 2.7149480E-10 1.3646576E-10 gauss-seidel spectral radius is 0.9825964 estimated iterations to convergence 62 setup time was (sec) 0.6400000 now iterating at: 19:42:46 rms-change max change #iterations 7.0976973E-02 13.86677 at 10iterations 4.6541989E-03 0.7726326 at 20iterations 3.1052020E-04 5.9652328E-02 at 30iterations 2.6367108E-05 4.6195984E-03 at 40iterations 4.8383476E-06 8.9216232E-04 at 50iterations finished qdiffx linear iterations at : 19:42:49 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 4.8383476E-06 8.9216232E-04 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 19:42:50 4.182u 0.287s 0:04.77 93.5% 0+0k 0+0io 6pf+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 19:42:50 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3055 !!! WARNING: TYR 265 has a net charge of -0.2720 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: 1.631556 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): -4.114000 61.34500 ymin,ymax (A): 13.54800 69.22000 zmin,zma (A): -13.29300 51.59600 x,y,z range (A): 65.45900 55.67200 64.88900 scale (grids/A): 1.631556 object centre (A): 28.61550 41.38400 19.15150 number of atom coordinates read : 3055 total number of charged atoms : 2915 net assigned charge : 4.228020 assigned positive charge : 454.6450 centred at (gu) : 94.37022 95.21009 91.99261 assigned negative charge : -450.4183 centred at (gu) : 94.44074 95.12650 92.21298 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 66669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33157 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18543 mr = 40885 m= 1929 mr = 11306 m= 61 mr = 761 m= 0 mr = 6 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 34244 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 381 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 22361 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) : 0.5438519 object centre at (A) : 28.61550 41.38400 19.15150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7746491E-02 1.6485745E-02 midg,1,midg; midg,igrid,midg -7.3300642E-03 -4.5684692E-03 1,midg,midg; igrid,midg,midg 2.0775178E-03 1.7166456E-03 gauss-seidel spectral radius is 0.9982024 estimated iterations to convergence 187 setup time was (sec) 0.9100000 now iterating at: 19:42:51 rms-change max change #iterations 3.311293 150.3873 at 10iterations 1.372658 55.79604 at 20iterations 0.5717496 23.98195 at 30iterations 0.2380647 8.824220 at 40iterations 9.8828875E-02 4.002078 at 50iterations 4.1319530E-02 1.775076 at 60iterations 1.7246138E-02 0.6343536 at 70iterations 7.1838400E-03 0.3130503 at 80iterations 2.9960149E-03 0.1107006 at 90iterations 1.2552367E-03 4.6880245E-02 at 100iterations 5.2525901E-04 2.0208597E-02 at 110iterations 2.1965816E-04 8.1052780E-03 at 120iterations finished qdiffx linear iterations at : 19:42:59 total time elapsed so far: 9.450000 # loops : 120 mean,max change (kT/e) : 2.1965816E-04 8.1052780E-03 energy calculations done at 9.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.620000 DelPhi exited at 19:43:00 9.626u 0.325s 0:10.46 95.0% 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 19:43:00 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3055 !!! WARNING: TYR 265 has a net charge of -0.2720 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: 2.447334 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): -4.114000 61.34500 ymin,ymax (A): 13.54800 69.22000 zmin,zma (A): -13.29300 51.59600 x,y,z range (A): 65.45900 55.67200 64.88900 scale (grids/A): 2.447334 object centre (A): 28.61550 41.38400 19.15150 number of atom coordinates read : 3055 total number of charged atoms : 2915 net assigned charge : 4.228020 assigned positive charge : 454.6450 centred at (gu) : 96.55501 97.81490 92.98867 assigned negative charge : -450.4183 centred at (gu) : 96.66099 97.68980 93.31951 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 154950 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33157 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 63818 mr = 101713 m= 17591 mr = 46615 m= 2871 mr = 12090 m= 175 mr = 1640 m= 3 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.8500001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.470000 number of dielectric boundary points 77282 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 23291 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) : 1.631556 object centre at (A) : 28.61550 41.38400 19.15150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1212026 0.2240660 midg,1,midg; midg,igrid,midg -9.2102535E-02 -9.3205944E-02 1,midg,midg; igrid,midg,midg -0.1119594 -1.4497420E-02 gauss-seidel spectral radius is 0.9991477 estimated iterations to convergence 271 setup time was (sec) 1.800000 now iterating at: 19:43:02 rms-change max change #iterations 8.789258 298.2088 at 10iterations 5.044415 153.9018 at 20iterations 2.855873 68.87985 at 30iterations 1.609969 39.50531 at 40iterations 0.9027020 20.50345 at 50iterations 0.5030363 13.50688 at 60iterations 0.2801626 6.732128 at 70iterations 0.1558126 3.904079 at 80iterations 8.6255327E-02 1.859541 at 90iterations 4.7762722E-02 1.048759 at 100iterations 2.6437370E-02 0.5541039 at 110iterations 1.4588770E-02 0.3129330 at 120iterations 8.0647999E-03 0.1702633 at 130iterations 4.4504669E-03 9.3513489E-02 at 140iterations 2.4526443E-03 5.5242538E-02 at 150iterations 1.3523662E-03 3.0035138E-02 at 160iterations 7.4473757E-04 1.5165329E-02 at 170iterations 4.1135529E-04 8.5198879E-03 at 180iterations finished qdiffx linear iterations at : 19:43:16 total time elapsed so far: 15.89000 # loops : 180 mean,max change (kT/e) : 4.1135529E-04 8.5198879E-03 energy calculations done at 15.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.06000 DelPhi exited at 19:43:17 16.064u 0.332s 0:16.84 97.3% 0+0k 0+0io 0pf+0w