Sun Oct 9 08:16:13 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 Sun Oct 9 2011 at 08:16:13 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 = 5273 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5502914 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): -16.96800 46.39300 ymin,ymax (A): 4.584000 69.23800 zmin,zma (A): -110.9990 -46.30600 x,y,z range (A): 63.36100 64.65400 64.69300 scale (grids/A): 0.5502914 object centre (A): 14.71250 36.91100 -78.65250 number of atom coordinates read : 5273 total number of charged atoms : 5107 net assigned charge : -3.499982 assigned positive charge : 791.5663 centred at (gu) : 90.74962 91.12460 89.10309 assigned negative charge : -795.0727 centred at (gu) : 90.72847 91.10906 88.97490 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 10344 nv = 96 ne = 84 npr = 105295 no. pairs analyzed = 105295 no. exposed pairs = 6988 no. arc points = 48275 no. surface atoms = 2332 nbur = 2941 mkacc time = 0.2300000 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 = 1.540000 m= 416 mr = 5264 m= 2 mr = 19 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 0.4900000 number of dielectric boundary points 5479 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4745 ## 562 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 13521 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5717823E-09 1.2070711E-09 midg,1,midg; midg,igrid,midg -3.5030273E-10 -3.2305020E-11 1,midg,midg; igrid,midg,midg -4.4849321E-10 6.3098145E-11 gauss-seidel spectral radius is 0.9831516 estimated iterations to convergence 63 setup time was (sec) 0.7200000 now iterating at: 08:16:14 rms-change max change #iterations 0.1029677 12.51546 at 10iterations 7.2857225E-03 0.9081993 at 20iterations 6.9754873E-04 0.1220131 at 30iterations 1.4152516E-04 2.6758194E-02 at 40iterations 4.1941094E-05 7.7934265E-03 at 50iterations finished qdiffx linear iterations at : 08:16:16 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 4.1941094E-05 7.7934265E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 08:16:17 3.560u 0.201s 0:04.13 91.0% 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 Sun Oct 9 2011 at 08:16:17 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 = 5273 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.650874 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): -16.96800 46.39300 ymin,ymax (A): 4.584000 69.23800 zmin,zma (A): -110.9990 -46.30600 x,y,z range (A): 63.36100 64.65400 64.69300 scale (grids/A): 1.650874 object centre (A): 14.71250 36.91100 -78.65250 number of atom coordinates read : 5273 total number of charged atoms : 5107 net assigned charge : -3.499982 assigned positive charge : 791.5663 centred at (gu) : 92.24762 93.37241 87.30750 assigned negative charge : -795.0727 centred at (gu) : 92.18507 93.32701 86.92453 start vw surface at 0.2100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 113645 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48275 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 35765 mr = 76645 m= 4045 mr = 24312 m= 117 mr = 2020 m= 0 mr = 13 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 81 time to turn everything in is 0.8000000 number of dielectric boundary points 50582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 484 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 39175 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) : 0.5502914 object centre at (A) : 14.71250 36.91100 -78.65250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9112193E-02 2.3998290E-02 midg,1,midg; midg,igrid,midg -8.6894250E-03 -7.3396005E-03 1,midg,midg; igrid,midg,midg -4.3359729E-03 -1.4784286E-02 gauss-seidel spectral radius is 0.9984588 estimated iterations to convergence 202 setup time was (sec) 1.110000 now iterating at: 08:16:18 rms-change max change #iterations 4.783712 164.0275 at 10iterations 2.118686 65.65183 at 20iterations 0.9463528 25.86485 at 30iterations 0.4238714 12.03140 at 40iterations 0.1889737 5.850827 at 50iterations 8.4575355E-02 2.718204 at 60iterations 3.7777919E-02 1.171954 at 70iterations 1.6922569E-02 0.5254517 at 80iterations 7.5855725E-03 0.2084312 at 90iterations 3.4015868E-03 9.2892647E-02 at 100iterations 1.5326376E-03 4.4857502E-02 at 110iterations 6.9479429E-04 1.9731522E-02 at 120iterations finished qdiffx linear iterations at : 08:16:25 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 6.9479429E-04 1.9731522E-02 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.190000 DelPhi exited at 08:16:26 8.189u 0.259s 0:08.80 95.7% 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 Sun Oct 9 2011 at 08:16:26 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 = 5273 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.476311 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): -16.96800 46.39300 ymin,ymax (A): 4.584000 69.23800 zmin,zma (A): -110.9990 -46.30600 x,y,z range (A): 63.36100 64.65400 64.69300 scale (grids/A): 2.476311 object centre (A): 14.71250 36.91100 -78.65250 number of atom coordinates read : 5273 total number of charged atoms : 5107 net assigned charge : -3.499982 assigned positive charge : 791.5663 centred at (gu) : 93.37099 95.05801 85.96078 assigned negative charge : -795.0727 centred at (gu) : 93.27750 94.99049 85.38664 start vw surface at 0.2000000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 263973 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48275 grid for indexing accessible points = 1.400000 m= 122923 mr = 188201 m= 36024 mr = 96028 m= 6490 mr = 26831 m= 541 mr = 4358 m= 11 mr = 270 m= 0 mr = 0 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 250 time to turn everything in is 1.940000 number of dielectric boundary points 114274 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 2.120000 number of grid points assigned charge 40820 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) : 1.650874 object centre at (A) : 14.71250 36.91100 -78.65250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9591527 0.2562165 midg,1,midg; midg,igrid,midg -1.1288054E-02 2.6611663E-02 1,midg,midg; igrid,midg,midg -0.2822451 9.6734829E-04 gauss-seidel spectral radius is 0.9992856 estimated iterations to convergence 295 setup time was (sec) 2.300000 now iterating at: 08:16:28 rms-change max change #iterations 12.33333 410.2507 at 10iterations 7.428503 175.5094 at 20iterations 4.459835 108.7326 at 30iterations 2.661252 58.99602 at 40iterations 1.573310 29.33266 at 50iterations 0.9314052 16.20755 at 60iterations 0.5496171 9.230978 at 70iterations 0.3232796 6.010635 at 80iterations 0.1894786 3.086899 at 90iterations 0.1110173 1.985473 at 100iterations 6.5036587E-02 1.114323 at 110iterations 3.8087286E-02 0.5904646 at 120iterations 2.2259535E-02 0.4063023 at 130iterations 1.3003817E-02 0.2276917 at 140iterations 7.5990353E-03 0.1196709 at 150iterations 4.4517429E-03 7.4355125E-02 at 160iterations 2.5997239E-03 4.1481972E-02 at 170iterations 1.5262569E-03 2.3920059E-02 at 180iterations finished qdiffx linear iterations at : 08:16:42 total time elapsed so far: 15.48000 # loops : 180 mean,max change (kT/e) : 1.5262569E-03 2.3920059E-02 energy calculations done at 15.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.66000 DelPhi exited at 08:16:42 15.658u 0.283s 0:16.26 97.9% 0+0k 0+0io 0pf+0w