Sat Oct 8 18:26:02 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 18:26:02 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 = 3573 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5548887 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): -19.97600 42.22300 ymin,ymax (A): -3.769000 56.52600 zmin,zma (A): 5.312000 69.46900 x,y,z range (A): 62.19900 60.29500 64.15701 scale (grids/A): 0.5548887 object centre (A): 11.12350 26.37850 37.39050 number of atom coordinates read : 3573 total number of charged atoms : 3429 net assigned charge : 9.000017 assigned positive charge : 536.2592 centred at (gu) : 90.03265 89.70267 90.39876 assigned negative charge : -527.2607 centred at (gu) : 90.12527 89.74203 90.38400 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7291 nv = 96 ne = 84 npr = 70217 no. pairs analyzed = 70217 no. exposed pairs = 4961 no. arc points = 35378 no. surface atoms = 1623 nbur = 1950 mkacc time = 0.1600000 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= 364 mr = 3563 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3516 ## 423 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9459 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7156840E-10 1.0452426E-09 midg,1,midg; midg,igrid,midg 1.3083686E-09 3.3319605E-10 1,midg,midg; igrid,midg,midg 1.7772492E-09 -2.3897076E-10 gauss-seidel spectral radius is 0.9833076 estimated iterations to convergence 64 setup time was (sec) 0.6400000 now iterating at: 18:26:03 rms-change max change #iterations 8.5534856E-02 13.91213 at 10iterations 6.4755338E-03 0.9468422 at 20iterations 8.8284811E-04 0.1240311 at 30iterations 2.1966564E-04 3.4175873E-02 at 40iterations 6.1539933E-05 9.6015930E-03 at 50iterations finished qdiffx linear iterations at : 18:26:06 total time elapsed so far: 4.210000 # loops : 50 mean,max change (kT/e) : 6.1539933E-05 9.6015930E-03 energy calculations done at 4.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 18:26:07 4.399u 0.308s 0:05.04 93.0% 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 Sat Oct 8 2011 at 18:26:07 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 = 3573 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: 1.664666 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): -19.97600 42.22300 ymin,ymax (A): -3.769000 56.52600 zmin,zma (A): 5.312000 69.46900 x,y,z range (A): 62.19900 60.29500 64.15701 scale (grids/A): 1.664666 object centre (A): 11.12350 26.37850 37.39050 number of atom coordinates read : 3573 total number of charged atoms : 3429 net assigned charge : 9.000017 assigned positive charge : 536.2592 centred at (gu) : 90.09644 89.10704 91.19541 assigned negative charge : -527.2607 centred at (gu) : 90.37561 89.22575 91.15169 start vw surface at 0.2000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 79332 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35378 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25838 mr = 51492 m= 3196 mr = 17423 m= 93 mr = 1661 m= 0 mr = 3 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 219 time to turn everything in is 0.6800000 number of dielectric boundary points 37880 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 337 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 26367 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) : 0.5548887 object centre at (A) : 11.12350 26.37850 37.39050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0626557E-02 1.0323779E-02 midg,1,midg; midg,igrid,midg 4.1493238E-03 4.4983081E-03 1,midg,midg; igrid,midg,midg 1.7083175E-02 -1.6292452E-03 gauss-seidel spectral radius is 0.9983345 estimated iterations to convergence 195 setup time was (sec) 1.020000 now iterating at: 18:26:08 rms-change max change #iterations 3.843708 148.5405 at 10iterations 1.652582 59.05018 at 20iterations 0.7166060 24.65215 at 30iterations 0.3095789 10.13495 at 40iterations 0.1343188 4.689873 at 50iterations 5.8191508E-02 2.110054 at 60iterations 2.5253674E-02 0.8463135 at 70iterations 1.1044273E-02 0.3755474 at 80iterations 4.8663975E-03 0.1615677 at 90iterations 2.1594733E-03 8.7612152E-02 at 100iterations 9.9028123E-04 3.3954620E-02 at 110iterations 4.7599021E-04 1.6074181E-02 at 120iterations finished qdiffx linear iterations at : 18:26:17 total time elapsed so far: 9.610000 # loops : 120 mean,max change (kT/e) : 4.7599021E-04 1.6074181E-02 energy calculations done at 9.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.790000 DelPhi exited at 18:26:17 9.788u 0.276s 0:10.34 97.1% 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 18:26:17 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 = 3573 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.496999 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): -19.97600 42.22300 ymin,ymax (A): -3.769000 56.52600 zmin,zma (A): 5.312000 69.46900 x,y,z range (A): 62.19900 60.29500 64.15701 scale (grids/A): 2.496999 object centre (A): 11.12350 26.37850 37.39050 number of atom coordinates read : 3573 total number of charged atoms : 3429 net assigned charge : 9.000017 assigned positive charge : 536.2592 centred at (gu) : 90.14435 88.66032 91.79274 assigned negative charge : -527.2607 centred at (gu) : 90.56332 88.83852 91.72746 start vw surface at 0.1500000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 183401 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35378 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 86543 mr = 126398 m= 27423 mr = 66867 m= 5253 mr = 20611 m= 387 mr = 3535 m= 8 mr = 167 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 735 time to turn everything in is 1.600000 number of dielectric boundary points 85437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 27410 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) : 1.664666 object centre at (A) : 11.12350 26.37850 37.39050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.3711557E-02 -5.3380981E-02 midg,1,midg; midg,igrid,midg -2.0329528E-02 8.5836008E-02 1,midg,midg; igrid,midg,midg 0.1772932 -3.8900699E-02 gauss-seidel spectral radius is 0.9992059 estimated iterations to convergence 280 setup time was (sec) 1.950000 now iterating at: 18:26:20 rms-change max change #iterations 9.925135 298.5267 at 10iterations 5.768095 128.4731 at 20iterations 3.327482 92.61643 at 30iterations 1.908629 40.85658 at 40iterations 1.090957 21.16893 at 50iterations 0.6211493 13.37617 at 60iterations 0.3540386 6.794411 at 70iterations 0.2003666 3.995468 at 80iterations 0.1138324 2.259987 at 90iterations 6.4378649E-02 1.272934 at 100iterations 3.6306538E-02 0.7167358 at 110iterations 2.0539999E-02 0.3965530 at 120iterations 1.1617995E-02 0.2345848 at 130iterations 6.5539619E-03 0.1205139 at 140iterations 3.6970598E-03 7.0266724E-02 at 150iterations 2.0932560E-03 3.9150238E-02 at 160iterations 1.1835579E-03 2.2766113E-02 at 170iterations 6.7039707E-04 1.2588501E-02 at 180iterations finished qdiffx linear iterations at : 18:26:34 total time elapsed so far: 15.80000 # loops : 180 mean,max change (kT/e) : 6.7039707E-04 1.2588501E-02 energy calculations done at 15.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.98000 DelPhi exited at 18:26:34 15.986u 0.299s 0:16.55 98.3% 0+0k 0+0io 0pf+0w