Mon Oct 10 14:37:57 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 Mon Oct 10 2011 at 14:37:57 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6189690 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): -23.13900 28.57500 ymin,ymax (A): -33.01400 24.50100 zmin,zma (A): -37.76700 18.26100 x,y,z range (A): 51.71400 57.51500 56.02800 scale (grids/A): 0.6189690 object centre (A): 2.718000 -4.256500 -9.752999 number of atom coordinates read : 2392 total number of charged atoms : 2237 net assigned charge : -1.999992 assigned positive charge : 351.2812 centred at (gu) : 89.78905 88.48192 89.78491 assigned negative charge : -353.2816 centred at (gu) : 89.99044 88.48508 89.74190 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6116 nv = 96 ne = 84 npr = 48646 no. pairs analyzed = 48646 no. exposed pairs = 3120 no. arc points = 21939 no. surface atoms = 1057 nbur = 1335 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 288 mr = 3155 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3231 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2172 ## 205 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7420 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3000057E-09 8.9225632E-10 midg,1,midg; midg,igrid,midg -1.9122826E-09 -1.2697506E-09 1,midg,midg; igrid,midg,midg 1.0457781E-08 -1.3011513E-08 gauss-seidel spectral radius is 0.9864689 estimated iterations to convergence 70 setup time was (sec) 0.6300000 now iterating at: 14:37:58 rms-change max change #iterations 0.1186032 18.73059 at 10iterations 1.0769477E-02 1.513277 at 20iterations 1.0028254E-03 0.1627226 at 30iterations 9.7491582E-05 1.6368866E-02 at 40iterations 1.1155981E-05 1.4953613E-03 at 50iterations finished qdiffx linear iterations at : 14:38:02 total time elapsed so far: 4.260000 # loops : 50 mean,max change (kT/e) : 1.1155981E-05 1.4953613E-03 energy calculations done at 4.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.440000 DelPhi exited at 14:38:02 4.439u 0.294s 0:05.04 93.6% 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 Mon Oct 10 2011 at 14:38:02 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.856907 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): -23.13900 28.57500 ymin,ymax (A): -33.01400 24.50100 zmin,zma (A): -37.76700 18.26100 x,y,z range (A): 51.71400 57.51500 56.02800 scale (grids/A): 1.856907 object centre (A): 2.718000 -4.256500 -9.752999 number of atom coordinates read : 2392 total number of charged atoms : 2237 net assigned charge : -1.999992 assigned positive charge : 351.2812 centred at (gu) : 89.36678 85.44562 89.35422 assigned negative charge : -353.2816 centred at (gu) : 89.97092 85.45514 89.22558 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 66488 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21939 grid for indexing accessible points = 1.400000 m= 22520 mr = 44916 m= 3009 mr = 15799 m= 147 mr = 1534 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 29880 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 190 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 17558 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) : 0.6189690 object centre at (A) : 2.718000 -4.256500 -9.752999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9806121E-02 -1.3302177E-03 midg,1,midg; midg,igrid,midg -1.6724089E-03 1.0211744E-02 1,midg,midg; igrid,midg,midg 8.9465221E-03 -3.5737332E-02 gauss-seidel spectral radius is 0.9985461 estimated iterations to convergence 208 setup time was (sec) 0.8300000 now iterating at: 14:38:03 rms-change max change #iterations 3.819280 173.3506 at 10iterations 1.736946 56.05991 at 20iterations 0.7959440 28.33270 at 30iterations 0.3617505 13.30493 at 40iterations 0.1657170 5.702015 at 50iterations 7.5719446E-02 2.676178 at 60iterations 3.4632783E-02 1.135593 at 70iterations 1.5804462E-02 0.5603333 at 80iterations 7.2505185E-03 0.2497711 at 90iterations 3.3127510E-03 0.1137371 at 100iterations 1.5271219E-03 5.2124023E-02 at 110iterations 7.0650404E-04 2.5745392E-02 at 120iterations finished qdiffx linear iterations at : 14:38:12 total time elapsed so far: 9.270000 # loops : 120 mean,max change (kT/e) : 7.0650404E-04 2.5745392E-02 energy calculations done at 9.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.460000 DelPhi exited at 14:38:13 9.458u 0.292s 0:10.25 95.0% 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 Mon Oct 10 2011 at 14:38:13 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.785360 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): -23.13900 28.57500 ymin,ymax (A): -33.01400 24.50100 zmin,zma (A): -37.76700 18.26100 x,y,z range (A): 51.71400 57.51500 56.02800 scale (grids/A): 2.785360 object centre (A): 2.718000 -4.256500 -9.752999 number of atom coordinates read : 2392 total number of charged atoms : 2237 net assigned charge : -1.999992 assigned positive charge : 351.2812 centred at (gu) : 89.05015 83.16827 89.03115 assigned negative charge : -353.2816 centred at (gu) : 89.95631 83.18260 88.83823 start vw surface at 0.1800000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 153779 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21939 grid for indexing accessible points = 1.400000 m= 74340 mr = 109485 m= 25030 mr = 59250 m= 5005 mr = 19080 m= 582 mr = 3246 m= 28 mr = 289 m= 3 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.430000 number of dielectric boundary points 67396 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 17896 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) : 1.856907 object centre at (A) : 2.718000 -4.256500 -9.752999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3191459 -2.6159968E-02 midg,1,midg; midg,igrid,midg -4.7509011E-02 0.1654998 1,midg,midg; igrid,midg,midg 5.4485738E-02 -0.3561879 gauss-seidel spectral radius is 0.9992353 estimated iterations to convergence 285 setup time was (sec) 1.820000 now iterating at: 14:38:15 rms-change max change #iterations 9.220332 374.7289 at 10iterations 5.416258 131.7318 at 20iterations 3.136352 69.90961 at 30iterations 1.816606 43.53849 at 40iterations 1.046235 22.48345 at 50iterations 0.6018462 15.16314 at 60iterations 0.3452553 7.125187 at 70iterations 0.1977669 5.366367 at 80iterations 0.1129703 2.169670 at 90iterations 6.4638369E-02 1.342945 at 100iterations 3.6931496E-02 0.7340832 at 110iterations 2.0995708E-02 0.4506350 at 120iterations 1.2046099E-02 0.2297916 at 130iterations 6.8673892E-03 0.1499043 at 140iterations 3.9136009E-03 8.3093643E-02 at 150iterations 2.2399991E-03 4.8927546E-02 at 160iterations 1.2824672E-03 2.9145241E-02 at 170iterations 7.4067112E-04 1.4080048E-02 at 180iterations finished qdiffx linear iterations at : 14:38:29 total time elapsed so far: 16.05000 # loops : 180 mean,max change (kT/e) : 7.4067112E-04 1.4080048E-02 energy calculations done at 16.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.27000 DelPhi exited at 14:38:30 16.272u 0.324s 0:17.16 96.6% 0+0k 0+0io 0pf+0w