Sat Oct 15 14:32:16 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 Sat Oct 15 2011 at 14:32:16 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 = 3008 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: 0.5918143 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): -8.964000 51.19000 ymin,ymax (A): -7.984000 39.92700 zmin,zma (A): -3.541000 53.35200 x,y,z range (A): 60.15400 47.91100 56.89300 scale (grids/A): 0.5918143 object centre (A): 21.11300 15.97150 24.90550 number of atom coordinates read : 3008 total number of charged atoms : 2866 net assigned charge : -3.499964 assigned positive charge : 452.2529 centred at (gu) : 89.24667 89.66072 89.34090 assigned negative charge : -455.7541 centred at (gu) : 89.15363 89.56007 89.25462 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6969 nv = 96 ne = 84 npr = 60162 no. pairs analyzed = 60162 no. exposed pairs = 3937 no. arc points = 27861 no. surface atoms = 1344 nbur = 1664 mkacc time = 0.1000000 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 = 1.484000 m= 317 mr = 3580 m= 0 mr = 16 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2200000 number of dielectric boundary points 3690 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2787 ## 271 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8750 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6187227E-09 1.4916735E-09 midg,1,midg; midg,igrid,midg -4.8144511E-09 2.0406783E-09 1,midg,midg; igrid,midg,midg -4.9941429E-09 1.6422426E-09 gauss-seidel spectral radius is 0.9852657 estimated iterations to convergence 68 setup time was (sec) 0.4300000 now iterating at: 14:32:17 rms-change max change #iterations 0.1086887 16.77920 at 10iterations 8.9411661E-03 1.372297 at 20iterations 7.3662354E-04 0.1100445 at 30iterations 6.3063264E-05 9.1724396E-03 at 40iterations 5.7691332E-06 8.6593628E-04 at 50iterations finished qdiffx linear iterations at : 14:32:23 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 5.7691332E-06 8.6593628E-04 energy calculations done at 3.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 14:32:23 3.732u 0.220s 0:06.79 58.1% 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 Sat Oct 15 2011 at 14:32:23 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 = 3008 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: 1.775443 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): -8.964000 51.19000 ymin,ymax (A): -7.984000 39.92700 zmin,zma (A): -3.541000 53.35200 x,y,z range (A): 60.15400 47.91100 56.89300 scale (grids/A): 1.775443 object centre (A): 21.11300 15.97150 24.90550 number of atom coordinates read : 3008 total number of charged atoms : 2866 net assigned charge : -3.499964 assigned positive charge : 452.2529 centred at (gu) : 87.73937 88.98152 88.02200 assigned negative charge : -455.7541 centred at (gu) : 87.46055 88.67989 87.76358 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75283 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27861 grid for indexing accessible points = 1.400000 m= 25230 mr = 50277 m= 3388 mr = 17814 m= 155 mr = 1811 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 479 time to turn everything in is 0.3800000 number of dielectric boundary points 34120 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 240 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 22326 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) : 0.5918143 object centre at (A) : 21.11300 15.97150 24.90550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3887351E-03 9.2232442E-03 midg,1,midg; midg,igrid,midg -2.2705333E-02 -2.0708278E-04 1,midg,midg; igrid,midg,midg -4.0499464E-02 2.5491616E-02 gauss-seidel spectral radius is 0.9984794 estimated iterations to convergence 203 setup time was (sec) 0.6100000 now iterating at: 14:32:24 rms-change max change #iterations 3.986618 182.1973 at 10iterations 1.773284 76.97615 at 20iterations 0.7953783 31.14210 at 30iterations 0.3581582 12.05147 at 40iterations 0.1597900 5.332184 at 50iterations 7.1622819E-02 2.467926 at 60iterations 3.2228403E-02 1.099414 at 70iterations 1.4434438E-02 0.5772533 at 80iterations 6.4947349E-03 0.2074366 at 90iterations 2.9066305E-03 9.3418121E-02 at 100iterations 1.3038720E-03 4.3672562E-02 at 110iterations 5.8646977E-04 1.9444466E-02 at 120iterations finished qdiffx linear iterations at : 14:32:34 total time elapsed so far: 8.460000 # loops : 120 mean,max change (kT/e) : 5.8646977E-04 1.9444466E-02 energy calculations done at 8.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.580000 DelPhi exited at 14:32:35 8.585u 0.301s 0:11.61 76.4% 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 Sat Oct 15 2011 at 14:32:35 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 = 3008 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: 2.663164 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): -8.964000 51.19000 ymin,ymax (A): -7.984000 39.92700 zmin,zma (A): -3.541000 53.35200 x,y,z range (A): 60.15400 47.91100 56.89300 scale (grids/A): 2.663164 object centre (A): 21.11300 15.97150 24.90550 number of atom coordinates read : 3008 total number of charged atoms : 2866 net assigned charge : -3.499964 assigned positive charge : 452.2529 centred at (gu) : 86.60880 88.47194 87.03271 assigned negative charge : -455.7541 centred at (gu) : 86.19072 88.01949 86.64533 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 174450 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27861 grid for indexing accessible points = 1.400000 m= 83441 mr = 122835 m= 27641 mr = 66390 m= 5684 mr = 21340 m= 612 mr = 3954 m= 33 mr = 339 m= 0 mr = 4 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 1912 time to turn everything in is 0.9900000 number of dielectric boundary points 76999 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 22924 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) : 1.775443 object centre at (A) : 21.11300 15.97150 24.90550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1588893 7.2550878E-02 midg,1,midg; midg,igrid,midg -0.2851996 2.5027040E-02 1,midg,midg; igrid,midg,midg -0.5630460 0.3727979 gauss-seidel spectral radius is 0.9992343 estimated iterations to convergence 285 setup time was (sec) 1.260000 now iterating at: 14:32:36 rms-change max change #iterations 9.938714 333.6179 at 10iterations 5.804515 130.2143 at 20iterations 3.364829 69.31066 at 30iterations 1.939955 42.93850 at 40iterations 1.115689 23.27304 at 50iterations 0.6400082 13.25214 at 60iterations 0.3653664 6.902886 at 70iterations 0.2087600 3.812489 at 80iterations 0.1191006 2.234226 at 90iterations 6.7917153E-02 1.261147 at 100iterations 3.8690411E-02 0.7348709 at 110iterations 2.2033473E-02 0.4512634 at 120iterations 1.2526527E-02 0.2495461 at 130iterations 7.1459189E-03 0.1313057 at 140iterations 4.0646475E-03 9.1003418E-02 at 150iterations 2.3140993E-03 4.0649414E-02 at 160iterations 1.3141065E-03 2.2979736E-02 at 170iterations 7.4788049E-04 1.4491081E-02 at 180iterations finished qdiffx linear iterations at : 14:32:53 total time elapsed so far: 13.96000 # loops : 180 mean,max change (kT/e) : 7.4788049E-04 1.4491081E-02 energy calculations done at 13.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.09000 DelPhi exited at 14:32:54 14.087u 0.328s 0:19.01 75.7% 0+0k 0+0io 0pf+0w