Sun Feb 12 05:06:42 PST 2012 #!/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_thin.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 Sun Feb 12 2012 at 05:06:43 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: 223 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2861 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: 0.5807315 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): -23.14500 19.83500 ymin,ymax (A): -41.04400 20.25800 zmin,zma (A): -22.57400 31.75800 x,y,z range (A): 42.98000 61.30200 54.33200 scale (grids/A): 0.5807315 object centre (A): -1.655001 -10.39300 4.592001 number of atom coordinates read : 2861 total number of charged atoms : 2651 net assigned charge : -0.4999969 assigned positive charge : 379.1896 centred at (gu) : 91.98788 90.39842 89.99960 assigned negative charge : -379.6906 centred at (gu) : 91.97378 90.25903 89.99861 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6279 nv = 96 ne = 84 npr = 63452 no. pairs analyzed = 63452 no. exposed pairs = 3497 no. arc points = 25078 no. surface atoms = 1186 nbur = 1675 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 = 1.456000 m= 305 mr = 3169 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2100000 number of dielectric boundary points 3394 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2418 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7900 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4669796E-10 -1.0868275E-10 midg,1,midg; midg,igrid,midg -2.5896660E-09 2.7522895E-09 1,midg,midg; igrid,midg,midg -2.5129443E-10 2.3411420E-10 gauss-seidel spectral radius is 0.9846923 estimated iterations to convergence 66 setup time was (sec) 0.4200000 now iterating at: 05:06:44 rms-change max change #iterations 9.2410594E-02 14.63583 at 10iterations 7.5275172E-03 1.325150 at 20iterations 8.3841156E-04 0.1533031 at 30iterations 1.7011967E-04 3.6262512E-02 at 40iterations 4.2732518E-05 9.2124939E-03 at 50iterations finished qdiffx linear iterations at : 05:06:47 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 4.2732518E-05 9.2124939E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 05:06:47 3.560u 0.186s 0:04.07 91.8% 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 Sun Feb 12 2012 at 05:06:47 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: 223 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2861 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: 1.742194 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): -23.14500 19.83500 ymin,ymax (A): -41.04400 20.25800 zmin,zma (A): -22.57400 31.75800 x,y,z range (A): 42.98000 61.30200 54.33200 scale (grids/A): 1.742194 object centre (A): -1.655001 -10.39300 4.592001 number of atom coordinates read : 2861 total number of charged atoms : 2651 net assigned charge : -0.4999969 assigned positive charge : 379.1896 centred at (gu) : 95.96297 91.19487 89.99844 assigned negative charge : -379.6906 centred at (gu) : 95.92087 90.77683 89.99566 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 68456 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25078 grid for indexing accessible points = 1.400000 m= 22916 mr = 45420 m= 3388 mr = 15997 m= 128 mr = 2035 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 414 time to turn everything in is 0.3500000 number of dielectric boundary points 31422 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 20616 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) : 0.5807315 object centre at (A) : -1.655001 -10.39300 4.592001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2750724E-03 -6.2060882E-03 midg,1,midg; midg,igrid,midg -7.5561199E-03 1.1541930E-02 1,midg,midg; igrid,midg,midg 8.3183066E-04 -1.0868098E-05 gauss-seidel spectral radius is 0.9984006 estimated iterations to convergence 198 setup time was (sec) 0.5900000 now iterating at: 05:06:48 rms-change max change #iterations 3.475368 144.4841 at 10iterations 1.518126 59.99752 at 20iterations 0.6673388 23.42209 at 30iterations 0.2942469 10.19078 at 40iterations 0.1292759 4.452499 at 50iterations 5.6760576E-02 1.911922 at 60iterations 2.5066907E-02 0.9045830 at 70iterations 1.1109374E-02 0.4041492 at 80iterations 4.9355337E-03 0.1725616 at 90iterations 2.2499831E-03 9.2575073E-02 at 100iterations 1.0460875E-03 3.5594940E-02 at 110iterations 5.0201541E-04 1.9683838E-02 at 120iterations finished qdiffx linear iterations at : 05:07:02 total time elapsed so far: 8.010000 # loops : 120 mean,max change (kT/e) : 5.0201541E-04 1.9683838E-02 energy calculations done at 8.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.140000 DelPhi exited at 05:07:03 8.143u 0.210s 0:15.53 53.7% 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 Sun Feb 12 2012 at 05:07:03 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: 223 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2861 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: 2.613292 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): -23.14500 19.83500 ymin,ymax (A): -41.04400 20.25800 zmin,zma (A): -22.57400 31.75800 x,y,z range (A): 42.98000 61.30200 54.33200 scale (grids/A): 2.613292 object centre (A): -1.655001 -10.39300 4.592001 number of atom coordinates read : 2861 total number of charged atoms : 2651 net assigned charge : -0.4999969 assigned positive charge : 379.1896 centred at (gu) : 98.94427 91.79211 89.99741 assigned negative charge : -379.6906 centred at (gu) : 98.88136 91.16518 89.99345 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 158884 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25078 grid for indexing accessible points = 1.400000 m= 74542 mr = 111523 m= 26551 mr = 58633 m= 5897 mr = 20690 m= 563 mr = 4300 m= 12 mr = 340 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 1371 time to turn everything in is 0.8600000 number of dielectric boundary points 70963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 21200 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) : 1.742194 object centre at (A) : -1.655001 -10.39300 4.592001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1307692 -9.7724073E-02 midg,1,midg; midg,igrid,midg -1.9363346E-02 9.4996832E-02 1,midg,midg; igrid,midg,midg 7.6986286E-03 -1.5848748E-02 gauss-seidel spectral radius is 0.9992009 estimated iterations to convergence 279 setup time was (sec) 1.120000 now iterating at: 05:07:04 rms-change max change #iterations 8.618462 277.5973 at 10iterations 4.935643 126.2623 at 20iterations 2.825163 63.99181 at 30iterations 1.604191 33.22490 at 40iterations 0.9096162 18.05415 at 50iterations 0.5146117 10.25180 at 60iterations 0.2902808 5.820982 at 70iterations 0.1637874 3.563207 at 80iterations 9.2301704E-02 2.097179 at 90iterations 5.2052118E-02 0.9901390 at 100iterations 2.9357955E-02 0.5956647 at 110iterations 1.6534925E-02 0.3096218 at 120iterations 9.3586519E-03 0.1660309 at 130iterations 5.3094132E-03 9.9128246E-02 at 140iterations 3.0469580E-03 5.9104919E-02 at 150iterations 1.7724459E-03 3.6645889E-02 at 160iterations 1.0579402E-03 2.3345947E-02 at 170iterations 6.5143028E-04 1.4701843E-02 at 180iterations finished qdiffx linear iterations at : 05:07:23 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 6.5143028E-04 1.4701843E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 05:07:24 13.097u 0.213s 0:21.06 63.1% 0+0k 0+0io 0pf+0w