Tue Oct 11 06:08:12 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+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 Oct 11 2011 at 06:08:12 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2035 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7477421 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): 3.444000 46.90600 ymin,ymax (A): 0.3579999 41.46400 zmin,zma (A): -2.721000 44.88900 x,y,z range (A): 43.46200 41.10600 47.61000 scale (grids/A): 0.7477421 object centre (A): 25.17500 20.91100 21.08400 number of atom coordinates read : 2035 total number of charged atoms : 1918 net assigned charge : 5.931007 assigned positive charge : 310.0851 centred at (gu) : 90.18220 90.28857 91.26531 assigned negative charge : -304.1542 centred at (gu) : 90.36527 90.25114 91.35190 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 7868 nv = 96 ne = 84 npr = 40701 no. pairs analyzed = 40701 no. exposed pairs = 2447 no. arc points = 16814 no. surface atoms = 840 nbur = 1195 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 596 mr = 4661 m= 8 mr = 133 m= 0 mr = 0 time to grow re-entrant surface = 7.9999991E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1408 ## 121 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 8244 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7627308E-07 3.1769563E-08 midg,1,midg; midg,igrid,midg 7.8844181E-08 1.7623384E-07 1,midg,midg; igrid,midg,midg 3.1706563E-07 -8.8037829E-08 gauss-seidel spectral radius is 0.9906639 estimated iterations to convergence 84 setup time was (sec) 0.3500000 now iterating at: 06:08:12 rms-change max change #iterations 0.2548313 28.49293 at 10iterations 3.5649944E-02 4.448135 at 20iterations 5.0282413E-03 0.6385484 at 30iterations 8.4550289E-04 0.1060600 at 40iterations 1.9428588E-04 2.5077820E-02 at 50iterations finished qdiffx linear iterations at : 06:08:15 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.9428588E-04 2.5077820E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 06:08:16 3.372u 0.182s 0:04.16 85.3% 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 Oct 11 2011 at 06:08:16 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2035 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.243226 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): 3.444000 46.90600 ymin,ymax (A): 0.3579999 41.46400 zmin,zma (A): -2.721000 44.88900 x,y,z range (A): 43.46200 41.10600 47.61000 scale (grids/A): 2.243226 object centre (A): 25.17500 20.91100 21.08400 number of atom coordinates read : 2035 total number of charged atoms : 1918 net assigned charge : 5.931007 assigned positive charge : 310.0851 centred at (gu) : 90.54643 90.86603 93.79585 assigned negative charge : -304.1542 centred at (gu) : 91.09565 90.75339 94.05585 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 82572 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16814 grid for indexing accessible points = 1.400000 m= 35258 mr = 59371 m= 7895 mr = 27392 m= 879 mr = 5598 m= 41 mr = 489 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 33788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 15280 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) : 0.7477421 object centre at (A) : 25.17500 20.91100 21.08400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2123709E-02 3.1748597E-02 midg,1,midg; midg,igrid,midg 3.2538995E-03 4.1486029E-02 1,midg,midg; igrid,midg,midg 5.9174154E-02 1.6568305E-02 gauss-seidel spectral radius is 0.9989319 estimated iterations to convergence 242 setup time was (sec) 0.6400000 now iterating at: 06:08:17 rms-change max change #iterations 5.017073 192.1851 at 10iterations 2.566959 84.84435 at 20iterations 1.318078 41.53213 at 30iterations 0.6779169 19.17395 at 40iterations 0.3483977 10.35532 at 50iterations 0.1782913 5.321945 at 60iterations 9.1032736E-02 3.005788 at 70iterations 4.6838835E-02 1.364418 at 80iterations 2.4097076E-02 0.6900787 at 90iterations 1.2453743E-02 0.3459425 at 100iterations 6.4773075E-03 0.1823254 at 110iterations 3.3991251E-03 0.1076946 at 120iterations finished qdiffx linear iterations at : 06:08:24 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 3.3991251E-03 0.1076946 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 06:08:24 7.933u 0.198s 0:08.45 96.0% 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 Tue Oct 11 2011 at 06:08:24 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2035 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.364839 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): 3.444000 46.90600 ymin,ymax (A): 0.3579999 41.46400 zmin,zma (A): -2.721000 44.88900 x,y,z range (A): 43.46200 41.10600 47.61000 scale (grids/A): 3.364839 object centre (A): 25.17500 20.91100 21.08400 number of atom coordinates read : 2035 total number of charged atoms : 1918 net assigned charge : 5.931007 assigned positive charge : 310.0851 centred at (gu) : 90.81952 91.29907 95.69373 assigned negative charge : -304.1542 centred at (gu) : 91.64358 91.13016 96.08378 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 190007 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16814 grid for indexing accessible points = 1.400000 m= 107059 mr = 142351 m= 47433 mr = 90188 m= 15349 mr = 39757 m= 3492 mr = 12334 m= 545 mr = 2643 m= 28 mr = 376 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 76252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 15344 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) : 2.243226 object centre at (A) : 25.17500 20.91100 21.08400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3156693 0.3686388 midg,1,midg; midg,igrid,midg -2.4903188E-02 0.3015376 1,midg,midg; igrid,midg,midg 0.4239429 0.3124999 gauss-seidel spectral radius is 0.9993188 estimated iterations to convergence 302 setup time was (sec) 1.540000 now iterating at: 06:08:26 rms-change max change #iterations 10.88771 273.1308 at 10iterations 6.535234 138.1882 at 20iterations 3.903139 96.66213 at 30iterations 2.328535 45.15165 at 40iterations 1.387200 27.97182 at 50iterations 0.8243646 15.23650 at 60iterations 0.4880909 9.258664 at 70iterations 0.2896194 4.699524 at 80iterations 0.1716812 3.056839 at 90iterations 0.1012184 1.708229 at 100iterations 6.0062520E-02 1.033623 at 110iterations 3.5730731E-02 0.5586982 at 120iterations 2.1351423E-02 0.3276062 at 130iterations 1.2896926E-02 0.2627602 at 140iterations 7.9610245E-03 0.1448593 at 150iterations 5.0836499E-03 8.7867737E-02 at 160iterations 3.3868270E-03 5.6800842E-02 at 170iterations 2.4066486E-03 4.0637970E-02 at 180iterations finished qdiffx linear iterations at : 06:08:38 total time elapsed so far: 13.01000 # loops : 180 mean,max change (kT/e) : 2.4066486E-03 4.0637970E-02 energy calculations done at 13.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 06:08:38 13.150u 0.226s 0:13.70 97.5% 0+0k 0+0io 0pf+0w