Sat Oct 8 18:23:10 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 8 2011 at 18:23:10 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 = 3793 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5304329 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): -1.743000 60.23200 ymin,ymax (A): -18.41900 48.69600 zmin,zma (A): -5.421000 58.90500 x,y,z range (A): 61.97500 67.11500 64.32600 scale (grids/A): 0.5304329 object centre (A): 29.24450 15.13850 26.74200 number of atom coordinates read : 3793 total number of charged atoms : 3643 net assigned charge : -6.999969 assigned positive charge : 572.5334 centred at (gu) : 88.81040 85.84212 90.58325 assigned negative charge : -579.5357 centred at (gu) : 88.86469 85.79612 90.57660 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6920 nv = 96 ne = 84 npr = 76208 no. pairs analyzed = 76208 no. exposed pairs = 4961 no. arc points = 34591 no. surface atoms = 1645 nbur = 2148 mkacc time = 0.2000000 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 = 1.596000 m= 277 mr = 3504 m= 2 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3692 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3495 ## 461 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9175 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1786419E-10 -2.1910838E-10 midg,1,midg; midg,igrid,midg -1.2768633E-09 -6.8459622E-12 1,midg,midg; igrid,midg,midg 4.4005716E-11 -3.5178815E-10 gauss-seidel spectral radius is 0.9817500 estimated iterations to convergence 61 setup time was (sec) 0.6800000 now iterating at: 18:23:12 rms-change max change #iterations 6.9427721E-02 13.95232 at 10iterations 4.3680728E-03 0.6387863 at 20iterations 3.2743393E-04 4.9189568E-02 at 30iterations 5.1231418E-05 1.1089325E-02 at 40iterations 1.2085337E-05 2.4609566E-03 at 50iterations finished qdiffx linear iterations at : 18:23:15 total time elapsed so far: 4.460000 # loops : 50 mean,max change (kT/e) : 1.2085337E-05 2.4609566E-03 energy calculations done at 4.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.640000 DelPhi exited at 18:23:16 4.648u 0.403s 0:05.31 94.9% 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 8 2011 at 18:23:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3793 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.591299 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): -1.743000 60.23200 ymin,ymax (A): -18.41900 48.69600 zmin,zma (A): -5.421000 58.90500 x,y,z range (A): 61.97500 67.11500 64.32600 scale (grids/A): 1.591299 object centre (A): 29.24450 15.13850 26.74200 number of atom coordinates read : 3793 total number of charged atoms : 3643 net assigned charge : -6.999969 assigned positive charge : 572.5334 centred at (gu) : 86.42995 77.52532 91.74865 assigned negative charge : -579.5357 centred at (gu) : 86.59383 77.38787 91.72939 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77256 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34591 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 23115 mr = 52126 m= 2195 mr = 15214 m= 59 mr = 907 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 34378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 386 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 27656 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) : 0.5304329 object centre at (A) : 29.24450 15.13850 26.74200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8501285E-04 -9.4234674E-05 midg,1,midg; midg,igrid,midg -2.8147846E-02 9.7264949E-04 1,midg,midg; igrid,midg,midg -8.1631262E-03 -2.1906167E-02 gauss-seidel spectral radius is 0.9981561 estimated iterations to convergence 185 setup time was (sec) 0.9900000 now iterating at: 18:23:17 rms-change max change #iterations 3.604435 136.1552 at 10iterations 1.483760 53.58035 at 20iterations 0.6140021 19.85625 at 30iterations 0.2547954 8.243159 at 40iterations 0.1055951 3.934737 at 50iterations 4.3818690E-02 1.535892 at 60iterations 1.8172003E-02 0.5806732 at 70iterations 7.5239134E-03 0.2697620 at 80iterations 3.1393429E-03 0.1141715 at 90iterations 1.3151343E-03 4.6012878E-02 at 100iterations 5.5882422E-04 1.9874573E-02 at 110iterations 2.4433815E-04 9.3080252E-03 at 120iterations finished qdiffx linear iterations at : 18:23:27 total time elapsed so far: 10.50000 # loops : 120 mean,max change (kT/e) : 2.4433815E-04 9.3080252E-03 energy calculations done at 10.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.67000 DelPhi exited at 18:23:27 10.676u 0.473s 0:11.42 97.5% 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 Sat Oct 8 2011 at 18:23:27 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 = 3793 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.386948 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): -1.743000 60.23200 ymin,ymax (A): -18.41900 48.69600 zmin,zma (A): -5.421000 58.90500 x,y,z range (A): 61.97500 67.11500 64.32600 scale (grids/A): 2.386948 object centre (A): 29.24450 15.13850 26.74200 number of atom coordinates read : 3793 total number of charged atoms : 3643 net assigned charge : -6.999969 assigned positive charge : 572.5334 centred at (gu) : 84.64450 71.28765 92.62273 assigned negative charge : -579.5357 centred at (gu) : 84.89068 71.08182 92.59392 start vw surface at 0.1300000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 179760 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34591 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 81264 mr = 128180 m= 21434 mr = 62964 m= 3154 mr = 15273 m= 164 mr = 1800 m= 4 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.570000 number of dielectric boundary points 77533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 29101 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) : 1.591299 object centre at (A) : 29.24450 15.13850 26.74200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2211966E-02 0.2037310 midg,1,midg; midg,igrid,midg -0.4709068 1.7966470E-02 1,midg,midg; igrid,midg,midg -0.1169233 -0.4330489 gauss-seidel spectral radius is 0.9991440 estimated iterations to convergence 270 setup time was (sec) 1.910000 now iterating at: 18:23:30 rms-change max change #iterations 9.487486 269.4130 at 10iterations 5.355583 147.5053 at 20iterations 2.999707 70.25452 at 30iterations 1.677224 36.33825 at 40iterations 0.9325459 18.45134 at 50iterations 0.5180500 11.02181 at 60iterations 0.2871378 7.070993 at 70iterations 0.1591437 3.404266 at 80iterations 8.7988243E-02 1.712669 at 90iterations 4.8604939E-02 1.014060 at 100iterations 2.6793158E-02 0.5197334 at 110iterations 1.4795255E-02 0.2840719 at 120iterations 8.1742350E-03 0.1672592 at 130iterations 4.5161955E-03 8.3641052E-02 at 140iterations 2.4978812E-03 5.1273346E-02 at 150iterations 1.3849232E-03 2.7334213E-02 at 160iterations 7.7449193E-04 1.6185045E-02 at 170iterations 4.3737542E-04 8.6441040E-03 at 180iterations finished qdiffx linear iterations at : 18:23:46 total time elapsed so far: 18.11000 # loops : 180 mean,max change (kT/e) : 4.3737542E-04 8.6441040E-03 energy calculations done at 18.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.27000 DelPhi exited at 18:23:46 18.273u 0.500s 0:19.06 98.4% 0+0k 0+0io 0pf+0w