Sun Oct 9 03:10:09 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 03:10:09 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4599 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: 0.5194427 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): 219.4690 276.0670 ymin,ymax (A): 71.68800 140.2230 zmin,zma (A): -69.72100 -6.084000 x,y,z range (A): 56.59798 68.53500 63.63700 scale (grids/A): 0.5194427 object centre (A): 247.7680 105.9555 -37.90250 number of atom coordinates read : 4599 total number of charged atoms : 4435 net assigned charge : 17.49999 assigned positive charge : 680.0995 centred at (gu) : 90.28114 87.44145 90.69984 assigned negative charge : -662.6049 centred at (gu) : 90.31424 87.44836 90.75057 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7783 nv = 96 ne = 84 npr = 92851 no. pairs analyzed = 92851 no. exposed pairs = 5968 no. arc points = 40472 no. surface atoms = 2045 nbur = 2554 mkacc time = 0.2200000 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 = 1.624000 m= 314 mr = 3920 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4164 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3972 ## 558 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 10430 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5025317E-10 2.2172553E-10 midg,1,midg; midg,igrid,midg 7.4707412E-10 1.8053330E-10 1,midg,midg; igrid,midg,midg 4.4481160E-10 2.6672634E-10 gauss-seidel spectral radius is 0.9810346 estimated iterations to convergence 60 setup time was (sec) 0.7100000 now iterating at: 03:10:10 rms-change max change #iterations 7.0307903E-02 12.05745 at 10iterations 6.0917786E-03 0.8938828 at 20iterations 1.4790907E-03 0.2186890 at 30iterations 4.5704405E-04 6.6509247E-02 at 40iterations 1.4317936E-04 2.0576477E-02 at 50iterations finished qdiffx linear iterations at : 03:10:13 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 1.4317936E-04 2.0576477E-02 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 03:10:14 4.273u 0.231s 0:04.88 92.2% 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 03:10:14 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4599 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: 1.558328 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): 219.4690 276.0670 ymin,ymax (A): 71.68800 140.2230 zmin,zma (A): -69.72100 -6.084000 x,y,z range (A): 56.59798 68.53500 63.63700 scale (grids/A): 1.558328 object centre (A): 247.7680 105.9555 -37.90250 number of atom coordinates read : 4599 total number of charged atoms : 4435 net assigned charge : 17.49999 assigned positive charge : 680.0995 centred at (gu) : 90.84161 82.32276 92.09781 assigned negative charge : -662.6049 centred at (gu) : 90.94241 82.34476 92.25124 start vw surface at 0.2300000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 86020 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40472 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 27197 mr = 57327 m= 2669 mr = 18376 m= 77 mr = 1245 m= 0 mr = 1 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 214 time to turn everything in is 0.7500000 number of dielectric boundary points 39014 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 503 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 33501 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) : 0.5194427 object centre at (A) : 247.7680 105.9555 -37.90250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1466581E-02 8.0242502E-03 midg,1,midg; midg,igrid,midg 3.3467386E-02 1.2083444E-02 1,midg,midg; igrid,midg,midg 2.8386065E-03 2.1958244E-03 gauss-seidel spectral radius is 0.9981701 estimated iterations to convergence 186 setup time was (sec) 1.060000 now iterating at: 03:10:15 rms-change max change #iterations 3.758078 139.1889 at 10iterations 1.554590 53.15919 at 20iterations 0.6450707 22.86438 at 30iterations 0.2679559 10.33298 at 40iterations 0.1119263 3.646290 at 50iterations 4.6781849E-02 1.537292 at 60iterations 1.9835223E-02 0.6738510 at 70iterations 8.5641090E-03 0.2858047 at 80iterations 3.8821946E-03 0.1219330 at 90iterations 1.8925746E-03 6.3838959E-02 at 100iterations 1.0222895E-03 3.4168243E-02 at 110iterations 6.0318835E-04 1.8203735E-02 at 120iterations finished qdiffx linear iterations at : 03:10:23 total time elapsed so far: 9.540000 # loops : 120 mean,max change (kT/e) : 6.0318835E-04 1.8203735E-02 energy calculations done at 9.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.720000 DelPhi exited at 03:10:24 9.722u 0.267s 0:10.26 97.2% 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 03:10:24 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4599 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: 2.337492 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): 219.4690 276.0670 ymin,ymax (A): 71.68800 140.2230 zmin,zma (A): -69.72100 -6.084000 x,y,z range (A): 56.59798 68.53500 63.63700 scale (grids/A): 2.337492 object centre (A): 247.7680 105.9555 -37.90250 number of atom coordinates read : 4599 total number of charged atoms : 4435 net assigned charge : 17.49999 assigned positive charge : 680.0995 centred at (gu) : 91.26186 78.48360 93.14634 assigned negative charge : -662.6049 centred at (gu) : 91.41348 78.51701 93.37698 start vw surface at 0.2000000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 199623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40472 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 92321 mr = 140704 m= 26852 mr = 71669 m= 4276 mr = 19991 m= 274 mr = 2646 m= 2 mr = 93 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 717 time to turn everything in is 1.620000 number of dielectric boundary points 88246 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 68 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 35406 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) : 1.558328 object centre at (A) : 247.7680 105.9555 -37.90250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5065187 6.5923914E-02 midg,1,midg; midg,igrid,midg 0.4697880 0.1778249 1,midg,midg; igrid,midg,midg 5.6263354E-02 1.1026783E-02 gauss-seidel spectral radius is 0.9991777 estimated iterations to convergence 275 setup time was (sec) 1.960000 now iterating at: 03:10:26 rms-change max change #iterations 10.21709 345.1878 at 10iterations 5.902708 151.3117 at 20iterations 3.383593 77.83321 at 30iterations 1.925471 41.27795 at 40iterations 1.089192 22.93756 at 50iterations 0.6151573 12.50433 at 60iterations 0.3472182 6.477215 at 70iterations 0.1946501 3.942690 at 80iterations 0.1093466 2.101082 at 90iterations 6.1320107E-02 1.139481 at 100iterations 3.4310814E-02 0.6184939 at 110iterations 1.9263141E-02 0.3492861 at 120iterations 1.0801516E-02 0.2100019 at 130iterations 6.0815909E-03 0.1062489 at 140iterations 3.4407552E-03 6.1769485E-02 at 150iterations 1.9656043E-03 4.3380737E-02 at 160iterations 1.1440179E-03 2.2567749E-02 at 170iterations 6.8339304E-04 1.3854027E-02 at 180iterations finished qdiffx linear iterations at : 03:10:40 total time elapsed so far: 15.50000 # loops : 180 mean,max change (kT/e) : 6.8339304E-04 1.3854027E-02 energy calculations done at 15.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.67000 DelPhi exited at 03:10:40 15.676u 0.273s 0:16.21 98.3% 0+0k 0+0io 0pf+0w