Tue Nov 22 14:21:05 PST 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 Nov 22 2011 at 14:21:08 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6422979 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): -5.274000 36.50300 ymin,ymax (A): -3.640000 48.67400 zmin,zma (A): -24.30100 31.12500 x,y,z range (A): 41.77700 52.31400 55.42600 scale (grids/A): 0.6422979 object centre (A): 15.61450 22.51700 3.412001 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 290.3020 centred at (gu) : 90.12931 92.56045 90.19591 assigned negative charge : -285.3023 centred at (gu) : 90.21627 92.64997 90.14407 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5612 nv = 96 ne = 84 npr = 39967 no. pairs analyzed = 39967 no. exposed pairs = 2504 no. arc points = 17553 no. surface atoms = 856 nbur = 1110 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 315 mr = 3110 m= 0 mr = 50 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2767 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1778 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6549 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1238956E-09 1.3160889E-08 midg,1,midg; midg,igrid,midg 9.3747072E-09 -8.1705331E-10 1,midg,midg; igrid,midg,midg 1.5336937E-08 8.4479673E-13 gauss-seidel spectral radius is 0.9873868 estimated iterations to convergence 73 setup time was (sec) 0.4400000 now iterating at: 14:21:08 rms-change max change #iterations 0.1285735 23.89083 at 10iterations 1.2962437E-02 2.032766 at 20iterations 1.2883921E-03 0.2104073 at 30iterations 1.2591502E-04 1.9180298E-02 at 40iterations 1.2715888E-05 2.0828247E-03 at 50iterations finished qdiffx linear iterations at : 14:21:16 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 1.2715888E-05 2.0828247E-03 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 14:21:18 3.228u 0.124s 0:10.58 31.5% 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 Nov 22 2011 at 14:21:20 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.926894 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): -5.274000 36.50300 ymin,ymax (A): -3.640000 48.67400 zmin,zma (A): -24.30100 31.12500 x,y,z range (A): 41.77700 52.31400 55.42600 scale (grids/A): 1.926894 object centre (A): 15.61450 22.51700 3.412001 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 290.3020 centred at (gu) : 90.38771 97.68114 90.58789 assigned negative charge : -285.3023 centred at (gu) : 90.64880 97.95021 90.43225 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 59768 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17553 grid for indexing accessible points = 1.400000 m= 22908 mr = 40934 m= 3744 mr = 17685 m= 205 mr = 2474 m= 1 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1167 time to turn everything in is 0.4100000 number of dielectric boundary points 25442 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 14449 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) : 0.6422979 object centre at (A) : 15.61450 22.51700 3.412001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1030928E-02 1.1945529E-02 midg,1,midg; midg,igrid,midg 3.3772223E-02 3.8817714E-03 1,midg,midg; igrid,midg,midg 8.0688316E-03 6.5926262E-03 gauss-seidel spectral radius is 0.9985909 estimated iterations to convergence 211 setup time was (sec) 0.6600000 now iterating at: 14:21:25 rms-change max change #iterations 3.661073 187.1794 at 10iterations 1.693935 60.41399 at 20iterations 0.7848518 29.04235 at 30iterations 0.3633414 12.70783 at 40iterations 0.1679310 6.092949 at 50iterations 7.7505872E-02 2.628621 at 60iterations 3.5799515E-02 1.343033 at 70iterations 1.6597908E-02 0.5821946 at 80iterations 7.6756282E-03 0.2638264 at 90iterations 3.5489525E-03 0.1415963 at 100iterations 1.6417095E-03 5.2276611E-02 at 110iterations 7.6212332E-04 2.8822422E-02 at 120iterations finished qdiffx linear iterations at : 14:21:42 total time elapsed so far: 6.500000 # loops : 120 mean,max change (kT/e) : 7.6212332E-04 2.8822422E-02 energy calculations done at 6.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.670000 DelPhi exited at 14:21:43 6.677u 0.155s 0:23.72 28.7% 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 Tue Nov 22 2011 at 14:21:45 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.890340 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): -5.274000 36.50300 ymin,ymax (A): -3.640000 48.67400 zmin,zma (A): -24.30100 31.12500 x,y,z range (A): 41.77700 52.31400 55.42600 scale (grids/A): 2.890340 object centre (A): 15.61450 22.51700 3.412001 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 290.3020 centred at (gu) : 90.58162 101.5216 90.88181 assigned negative charge : -285.3023 centred at (gu) : 90.97333 101.9254 90.64838 start vw surface at 0.1100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 138044 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17553 grid for indexing accessible points = 1.400000 m= 72160 mr = 99061 m= 28398 mr = 60161 m= 6816 mr = 23813 m= 991 mr = 5266 m= 64 mr = 692 m= 0 mr = 40 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 4111 time to turn everything in is 1.050000 number of dielectric boundary points 57440 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 14670 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) : 1.926894 object centre at (A) : 15.61450 22.51700 3.412001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9367433 1.3185871E-02 midg,1,midg; midg,igrid,midg 0.3674519 -3.7974052E-02 1,midg,midg; igrid,midg,midg 5.0345272E-02 0.1231418 gauss-seidel spectral radius is 0.9992333 estimated iterations to convergence 285 setup time was (sec) 1.320000 now iterating at: 14:21:52 rms-change max change #iterations 8.631953 466.8986 at 10iterations 4.957233 127.6176 at 20iterations 2.821466 60.22422 at 30iterations 1.607087 32.33744 at 40iterations 0.9153305 20.18337 at 50iterations 0.5208614 11.42861 at 60iterations 0.2958044 6.195496 at 70iterations 0.1680093 3.255774 at 80iterations 9.5354877E-02 1.896707 at 90iterations 5.4115377E-02 1.147119 at 100iterations 3.0676665E-02 0.5970469 at 110iterations 1.7438890E-02 0.3383293 at 120iterations 9.8928483E-03 0.1959953 at 130iterations 5.6225313E-03 0.1068726 at 140iterations 3.1919414E-03 6.0348511E-02 at 150iterations 1.8123470E-03 3.8284302E-02 at 160iterations 1.0301409E-03 2.2774696E-02 at 170iterations 5.8432267E-04 1.1106491E-02 at 180iterations finished qdiffx linear iterations at : 14:22:19 total time elapsed so far: 10.39000 # loops : 180 mean,max change (kT/e) : 5.8432267E-04 1.1106491E-02 energy calculations done at 10.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.56000 DelPhi exited at 14:22:20 10.561u 0.154s 0:35.72 29.9% 0+0k 0+0io 0pf+0w