Tue Oct 11 03:16:59 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 Tue Oct 11 2011 at 03:16:59 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 = 3271 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5436360 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): 5.999000 62.63100 ymin,ymax (A): -7.260000 58.22500 zmin,zma (A): 58.94800 112.6090 x,y,z range (A): 56.63200 65.48500 53.66100 scale (grids/A): 0.5436360 object centre (A): 34.31500 25.48250 85.77850 number of atom coordinates read : 3271 total number of charged atoms : 3170 net assigned charge : -4.999980 assigned positive charge : 500.7633 centred at (gu) : 91.00957 91.47328 88.54478 assigned negative charge : -505.7647 centred at (gu) : 90.98335 91.51735 88.58422 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6308 nv = 96 ne = 84 npr = 62958 no. pairs analyzed = 62958 no. exposed pairs = 4959 no. arc points = 34283 no. surface atoms = 1640 nbur = 1631 mkacc time = 0.1800000 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= 255 mr = 2796 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3367 ## 399 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 8364 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2676122E-11 -3.8952602E-10 midg,1,midg; midg,igrid,midg 9.0820814E-12 -8.4961543E-10 1,midg,midg; igrid,midg,midg -3.6296294E-10 -1.2982129E-10 gauss-seidel spectral radius is 0.9825918 estimated iterations to convergence 62 setup time was (sec) 0.7200000 now iterating at: 03:17:00 rms-change max change #iterations 7.2970554E-02 11.57452 at 10iterations 4.8486539E-03 0.7214203 at 20iterations 4.6333621E-04 9.4398499E-02 at 30iterations 1.0098435E-04 2.3134232E-02 at 40iterations 2.8853183E-05 6.5956116E-03 at 50iterations finished qdiffx linear iterations at : 03:17:03 total time elapsed so far: 4.020000 # loops : 50 mean,max change (kT/e) : 2.8853183E-05 6.5956116E-03 energy calculations done at 4.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 03:17:04 4.255u 0.220s 0:04.78 93.5% 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 Tue Oct 11 2011 at 03:17:04 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 = 3271 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: 1.630908 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): 5.999000 62.63100 ymin,ymax (A): -7.260000 58.22500 zmin,zma (A): 58.94800 112.6090 x,y,z range (A): 56.63200 65.48500 53.66100 scale (grids/A): 1.630908 object centre (A): 34.31500 25.48250 85.77850 number of atom coordinates read : 3271 total number of charged atoms : 3170 net assigned charge : -4.999980 assigned positive charge : 500.7633 centred at (gu) : 93.02760 94.41872 85.63341 assigned negative charge : -505.7647 centred at (gu) : 92.94949 94.55148 85.75200 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 68728 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34283 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 20152 mr = 42510 m= 2084 mr = 12659 m= 60 mr = 884 m= 0 mr = 5 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 34966 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 332 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 24285 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) : 0.5436360 object centre at (A) : 34.31500 25.48250 85.77850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0870778E-02 -1.7227744E-03 midg,1,midg; midg,igrid,midg 3.0943765E-03 -5.1341608E-02 1,midg,midg; igrid,midg,midg -1.5443332E-02 -1.2001334E-02 gauss-seidel spectral radius is 0.9982346 estimated iterations to convergence 189 setup time was (sec) 1.040000 now iterating at: 03:17:05 rms-change max change #iterations 3.557211 155.3577 at 10iterations 1.499454 67.71982 at 20iterations 0.6301687 22.98099 at 30iterations 0.2653522 9.571140 at 40iterations 0.1116964 3.871029 at 50iterations 4.6930894E-02 1.633606 at 60iterations 1.9793080E-02 0.7478904 at 70iterations 8.3887773E-03 0.3003006 at 80iterations 3.5664800E-03 0.1378975 at 90iterations 1.5161531E-03 5.2883148E-02 at 100iterations 6.5829448E-04 2.6728630E-02 at 110iterations 2.9579524E-04 1.1220932E-02 at 120iterations finished qdiffx linear iterations at : 03:17:13 total time elapsed so far: 9.340000 # loops : 120 mean,max change (kT/e) : 2.9579524E-04 1.1220932E-02 energy calculations done at 9.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.580000 DelPhi exited at 03:17:14 9.583u 0.223s 0:10.12 96.8% 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 Tue Oct 11 2011 at 03:17:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3271 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: 2.446362 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): 5.999000 62.63100 ymin,ymax (A): -7.260000 58.22500 zmin,zma (A): 58.94800 112.6090 x,y,z range (A): 56.63200 65.48500 53.66100 scale (grids/A): 2.446362 object centre (A): 34.31500 25.48250 85.77850 number of atom coordinates read : 3271 total number of charged atoms : 3170 net assigned charge : -4.999980 assigned positive charge : 500.7633 centred at (gu) : 94.54114 96.62785 83.44979 assigned negative charge : -505.7647 centred at (gu) : 94.42417 96.82701 83.62777 start vw surface at 0.2100000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 159489 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34283 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 68446 mr = 105565 m= 19858 mr = 50662 m= 3174 mr = 14043 m= 241 mr = 1872 m= 3 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.600000 number of dielectric boundary points 78968 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 25332 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) : 1.630908 object centre at (A) : 34.31500 25.48250 85.77850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1747838 -9.6834116E-03 midg,1,midg; midg,igrid,midg 0.3018686 -1.016393 1,midg,midg; igrid,midg,midg -0.2456972 -0.1795017 gauss-seidel spectral radius is 0.9991868 estimated iterations to convergence 277 setup time was (sec) 1.980000 now iterating at: 03:17:16 rms-change max change #iterations 9.630663 346.1700 at 10iterations 5.657495 156.4762 at 20iterations 3.278201 92.97029 at 30iterations 1.880264 45.62303 at 40iterations 1.074666 26.66275 at 50iterations 0.6122473 14.24738 at 60iterations 0.3477420 7.593929 at 70iterations 0.1963201 4.151585 at 80iterations 0.1105423 2.366108 at 90iterations 6.2332783E-02 1.321782 at 100iterations 3.5107724E-02 0.7491989 at 110iterations 1.9737452E-02 0.4264664 at 120iterations 1.1099565E-02 0.2218781 at 130iterations 6.2414245E-03 0.1340872 at 140iterations 3.5173562E-03 7.7293396E-02 at 150iterations 1.9860708E-03 4.3632507E-02 at 160iterations 1.1300716E-03 2.3963928E-02 at 170iterations 6.5140164E-04 1.4593124E-02 at 180iterations finished qdiffx linear iterations at : 03:17:29 total time elapsed so far: 15.10000 # loops : 180 mean,max change (kT/e) : 6.5140164E-04 1.4593124E-02 energy calculations done at 15.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.34000 DelPhi exited at 03:17:30 15.343u 0.250s 0:15.88 98.1% 0+0k 0+0io 0pf+0w