Wed Dec 21 14:20:57 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+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 Wed Dec 21 2011 at 14:20:58 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 = 1948 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: 0.5557637 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): -35.28800 12.48300 ymin,ymax (A): -1.056000 41.86700 zmin,zma (A): -2.576000 61.48000 x,y,z range (A): 47.77100 42.92300 64.05600 scale (grids/A): 0.5557637 object centre (A): -11.40250 20.40550 29.45200 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 4.000004 assigned positive charge : 285.3841 centred at (gu) : 89.71914 90.12904 89.19955 assigned negative charge : -281.3843 centred at (gu) : 89.62190 90.30716 89.16840 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4157 nv = 96 ne = 84 npr = 38349 no. pairs analyzed = 38349 no. exposed pairs = 2526 no. arc points = 18085 no. surface atoms = 858 nbur = 1090 mkacc time = 0.1100000 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 = 1.568000 m= 155 mr = 2134 m= 0 mr = 8 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 2170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1855 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 5138 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1666444E-10 4.5940982E-10 midg,1,midg; midg,igrid,midg 1.3749729E-09 -7.5203632E-10 1,midg,midg; igrid,midg,midg -2.4101923E-10 8.8560936E-10 gauss-seidel spectral radius is 0.9832256 estimated iterations to convergence 64 setup time was (sec) 0.5300000 now iterating at: 14:20:58 rms-change max change #iterations 6.3043050E-02 12.45218 at 10iterations 4.3353094E-03 0.9455147 at 20iterations 3.0154819E-04 6.5639496E-02 at 30iterations 2.1057644E-05 4.1519403E-03 at 40iterations 1.4715049E-06 3.0517578E-04 at 50iterations finished qdiffx linear iterations at : 14:21:02 total time elapsed so far: 3.810000 # loops : 50 mean,max change (kT/e) : 1.4715049E-06 3.0517578E-04 energy calculations done at 3.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.980000 DelPhi exited at 14:21:02 3.984u 0.276s 0:04.58 92.7% 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 Wed Dec 21 2011 at 14:21:02 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 = 1948 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: 1.667291 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): -35.28800 12.48300 ymin,ymax (A): -1.056000 41.86700 zmin,zma (A): -2.576000 61.48000 x,y,z range (A): 47.77100 42.92300 64.05600 scale (grids/A): 1.667291 object centre (A): -11.40250 20.40550 29.45200 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 4.000004 assigned positive charge : 285.3841 centred at (gu) : 89.15740 90.38741 87.59856 assigned negative charge : -281.3843 centred at (gu) : 88.86593 90.92177 87.50526 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 45037 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18085 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 14984 mr = 30076 m= 1689 mr = 10840 m= 42 mr = 941 m= 0 mr = 1 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 273 time to turn everything in is 0.4300000 number of dielectric boundary points 19894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 14008 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) : 0.5557637 object centre at (A) : -11.40250 20.40550 29.45200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0877212E-02 1.9725308E-02 midg,1,midg; midg,igrid,midg 5.4172371E-03 -7.3623541E-03 1,midg,midg; igrid,midg,midg -1.6083671E-03 1.6787107E-03 gauss-seidel spectral radius is 0.9981467 estimated iterations to convergence 185 setup time was (sec) 0.7100000 now iterating at: 14:21:03 rms-change max change #iterations 2.702723 151.2933 at 10iterations 1.107588 48.22399 at 20iterations 0.4563848 20.51291 at 30iterations 0.1885245 8.749548 at 40iterations 7.7876531E-02 3.526928 at 50iterations 3.2108743E-02 1.430765 at 60iterations 1.3302020E-02 0.5570755 at 70iterations 5.4829661E-03 0.2870483 at 80iterations 2.2636664E-03 9.8237991E-02 at 90iterations 9.3340426E-04 3.8116455E-02 at 100iterations 3.8564354E-04 1.6387939E-02 at 110iterations 1.5898922E-04 6.5488815E-03 at 120iterations finished qdiffx linear iterations at : 14:21:13 total time elapsed so far: 10.67000 # loops : 120 mean,max change (kT/e) : 1.5898922E-04 6.5488815E-03 energy calculations done at 10.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.85000 DelPhi exited at 14:21:14 10.851u 0.353s 0:11.85 94.5% 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 Wed Dec 21 2011 at 14:21:14 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 = 1948 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: 2.500937 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): -35.28800 12.48300 ymin,ymax (A): -1.056000 41.86700 zmin,zma (A): -2.576000 61.48000 x,y,z range (A): 47.77100 42.92300 64.05600 scale (grids/A): 2.500937 object centre (A): -11.40250 20.40550 29.45200 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 4.000004 assigned positive charge : 285.3841 centred at (gu) : 88.73606 90.58114 86.39784 assigned negative charge : -281.3843 centred at (gu) : 88.29890 91.38271 86.25788 start vw surface at 0.1600000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 104459 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18085 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 50119 mr = 73472 m= 16026 mr = 40429 m= 2784 mr = 12746 m= 213 mr = 1983 m= 5 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 793 time to turn everything in is 1.090000 number of dielectric boundary points 44879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 14538 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) : 1.667291 object centre at (A) : -11.40250 20.40550 29.45200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2809787 0.2038405 midg,1,midg; midg,igrid,midg 6.0274366E-02 -0.1175486 1,midg,midg; igrid,midg,midg -4.2320296E-02 2.2441620E-02 gauss-seidel spectral radius is 0.9990947 estimated iterations to convergence 263 setup time was (sec) 1.500000 now iterating at: 14:21:16 rms-change max change #iterations 6.771753 269.6778 at 10iterations 3.679682 101.3237 at 20iterations 1.995617 50.10548 at 30iterations 1.077921 26.75887 at 40iterations 0.5833127 13.55147 at 50iterations 0.3154855 7.913126 at 60iterations 0.1700196 4.231221 at 70iterations 9.1750637E-02 2.326411 at 80iterations 4.9538717E-02 1.241793 at 90iterations 2.6699429E-02 0.6251450 at 100iterations 1.4391202E-02 0.3540506 at 110iterations 7.7924179E-03 0.1891260 at 120iterations 4.2043040E-03 0.1028252 at 130iterations 2.2685041E-03 5.6915283E-02 at 140iterations 1.2239589E-03 2.7717590E-02 at 150iterations 6.5912824E-04 1.8013000E-02 at 160iterations 3.5657559E-04 8.9645386E-03 at 170iterations 1.9249269E-04 5.0601959E-03 at 180iterations finished qdiffx linear iterations at : 14:21:31 total time elapsed so far: 16.76000 # loops : 180 mean,max change (kT/e) : 1.9249269E-04 5.0601959E-03 energy calculations done at 16.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.95000 DelPhi exited at 14:21:35 16.951u 0.479s 0:20.55 84.7% 0+0k 0+0io 0pf+0w