Sat Oct 15 13:58:00 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 13:58:05 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4333 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5095541 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): -15.72000 37.33500 ymin,ymax (A): -32.58800 31.54600 zmin,zma (A): -3.816000 66.04900 x,y,z range (A): 53.05500 64.13400 69.86501 scale (grids/A): 0.5095541 object centre (A): 10.80750 -0.5210009 31.11650 number of atom coordinates read : 4333 total number of charged atoms : 4131 net assigned charge : -9.9968195E-02 assigned positive charge : 648.0361 centred at (gu) : 89.90376 90.87914 87.51878 assigned negative charge : -648.1403 centred at (gu) : 89.78994 90.95042 87.63497 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7110 nv = 96 ne = 84 npr = 87903 no. pairs analyzed = 87903 no. exposed pairs = 5735 no. arc points = 39936 no. surface atoms = 1897 nbur = 2436 mkacc time = 0.2400000 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 = 1.680000 m= 280 mr = 3579 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 3803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3862 ## 597 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 9576 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8900467E-10 -1.4002331E-10 midg,1,midg; midg,igrid,midg 1.1959309E-10 -2.1165140E-10 1,midg,midg; igrid,midg,midg -2.7122393E-10 2.3757976E-10 gauss-seidel spectral radius is 0.9802737 estimated iterations to convergence 59 setup time was (sec) 0.8000000 now iterating at: 13:58:10 rms-change max change #iterations 6.3499898E-02 10.03746 at 10iterations 3.6410971E-03 0.6576700 at 20iterations 2.2577062E-04 3.5652161E-02 at 30iterations 2.8075228E-05 5.5236816E-03 at 40iterations 6.7364695E-06 9.7465515E-04 at 50iterations finished qdiffx linear iterations at : 13:58:24 total time elapsed so far: 5.670000 # loops : 50 mean,max change (kT/e) : 6.7364695E-06 9.7465515E-04 energy calculations done at 5.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.850000 DelPhi exited at 13:58:27 5.853u 0.433s 0:22.52 27.8% 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 13:58:29 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4333 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.528662 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): -15.72000 37.33500 ymin,ymax (A): -32.58800 31.54600 zmin,zma (A): -3.816000 66.04900 x,y,z range (A): 53.05500 64.13400 69.86501 scale (grids/A): 1.528662 object centre (A): 10.80750 -0.5210009 31.11650 number of atom coordinates read : 4333 total number of charged atoms : 4131 net assigned charge : -9.9968195E-02 assigned positive charge : 648.0361 centred at (gu) : 89.71022 92.63618 82.55520 assigned negative charge : -648.1403 centred at (gu) : 89.36966 92.85088 82.90475 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 79496 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39936 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 22837 mr = 53274 m= 2035 mr = 14833 m= 41 mr = 844 m= 0 mr = 4 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 333 time to turn everything in is 0.7300000 number of dielectric boundary points 35454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 521 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 31079 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) : 0.5095541 object centre at (A) : 10.80750 -0.5210009 31.11650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3660440E-03 -1.3321583E-02 midg,1,midg; midg,igrid,midg -1.3806336E-03 -1.3537498E-02 1,midg,midg; igrid,midg,midg -2.1025427E-03 8.6997496E-03 gauss-seidel spectral radius is 0.9980617 estimated iterations to convergence 181 setup time was (sec) 1.130000 now iterating at: 13:58:31 rms-change max change #iterations 3.565729 149.9686 at 10iterations 1.433917 53.16124 at 20iterations 0.5802098 18.68077 at 30iterations 0.2360050 8.039158 at 40iterations 9.5185295E-02 3.428043 at 50iterations 3.8524542E-02 1.488144 at 60iterations 1.5669538E-02 0.5511780 at 70iterations 6.3597108E-03 0.2163677 at 80iterations 2.5892011E-03 9.3450546E-02 at 90iterations 1.0498676E-03 3.4805298E-02 at 100iterations 4.3114086E-04 1.5522957E-02 at 110iterations 1.7934028E-04 6.5937042E-03 at 120iterations finished qdiffx linear iterations at : 13:59:03 total time elapsed so far: 13.13000 # loops : 120 mean,max change (kT/e) : 1.7934028E-04 6.5937042E-03 energy calculations done at 13.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.31000 DelPhi exited at 13:59:04 13.315u 0.544s 0:35.54 38.9% 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 13:59:05 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4333 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.292994 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): -15.72000 37.33500 ymin,ymax (A): -32.58800 31.54600 zmin,zma (A): -3.816000 66.04900 x,y,z range (A): 53.05500 64.13400 69.86501 scale (grids/A): 2.292994 object centre (A): 10.80750 -0.5210009 31.11650 number of atom coordinates read : 4333 total number of charged atoms : 4131 net assigned charge : -9.9968195E-02 assigned positive charge : 648.0361 centred at (gu) : 89.56506 93.95397 78.83260 assigned negative charge : -648.1403 centred at (gu) : 89.05425 94.27622 79.35693 start vw surface at 0.1800000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 185225 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39936 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 80953 mr = 131149 m= 20434 mr = 62094 m= 2859 mr = 14417 m= 144 mr = 1733 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 1155 time to turn everything in is 1.730000 number of dielectric boundary points 80166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 32943 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) : 1.528662 object centre at (A) : 10.80750 -0.5210009 31.11650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1543595 -0.2819171 midg,1,midg; midg,igrid,midg -7.9547785E-02 -0.2894669 1,midg,midg; igrid,midg,midg -2.9271390E-02 0.1355580 gauss-seidel spectral radius is 0.9991387 estimated iterations to convergence 269 setup time was (sec) 2.140000 now iterating at: 13:59:10 rms-change max change #iterations 9.644285 261.9507 at 10iterations 5.476840 147.2882 at 20iterations 3.083309 73.34406 at 30iterations 1.734081 41.33219 at 40iterations 0.9690446 20.78898 at 50iterations 0.5396504 12.63530 at 60iterations 0.3001913 7.349062 at 70iterations 0.1663768 3.922050 at 80iterations 9.2202827E-02 2.025458 at 90iterations 5.0997060E-02 1.089844 at 100iterations 2.8176989E-02 0.5590882 at 110iterations 1.5570594E-02 0.3271594 at 120iterations 8.6079743E-03 0.1954894 at 130iterations 4.7430880E-03 9.5497370E-02 at 140iterations 2.6132041E-03 5.4234505E-02 at 150iterations 1.4440642E-03 2.9715538E-02 at 160iterations 7.9575396E-04 1.5228271E-02 at 170iterations 4.4041011E-04 9.7503662E-03 at 180iterations finished qdiffx linear iterations at : 14:00:01 total time elapsed so far: 22.65000 # loops : 180 mean,max change (kT/e) : 4.4041011E-04 9.7503662E-03 energy calculations done at 22.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.82000 DelPhi exited at 14:00:02 22.821u 0.580s 0:57.59 40.6% 0+0k 0+0io 0pf+0w