Sat Oct 15 14:13:44 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+sph2.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 = amb2.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 15 2011 at 14:13:44 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4581 !!! WARNING: HEM 810 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5227453 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): -24.71100 40.01300 ymin,ymax (A): -18.17800 46.73200 zmin,zma (A): 7.104001 75.20600 x,y,z range (A): 64.72400 64.91000 68.10200 scale (grids/A): 0.5227453 object centre (A): 7.651000 14.27700 41.15500 number of atom coordinates read : 4581 total number of charged atoms : 4341 net assigned charge : 7.800027 assigned positive charge : 695.0057 centred at (gu) : 91.39269 88.94422 87.71333 assigned negative charge : -687.2094 centred at (gu) : 91.49854 89.04908 87.57642 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8145 nv = 96 ne = 84 npr = 91079 no. pairs analyzed = 91079 no. exposed pairs = 6090 no. arc points = 41631 no. surface atoms = 2037 nbur = 2544 mkacc time = 0.1500000 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= 304 mr = 4159 m= 0 mr = 8 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4282 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4062 ## 578 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 10598 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8516681E-10 4.2038434E-10 midg,1,midg; midg,igrid,midg 8.2443319E-10 -1.7479045E-10 1,midg,midg; igrid,midg,midg 4.4128995E-10 -3.4631112E-10 gauss-seidel spectral radius is 0.9812734 estimated iterations to convergence 60 setup time was (sec) 0.5200000 now iterating at: 14:13:45 rms-change max change #iterations 7.4993797E-02 10.08891 at 10iterations 4.8823748E-03 0.6395111 at 20iterations 8.6261996E-04 0.1184759 at 30iterations 3.3886029E-04 5.0964355E-02 at 40iterations 1.4171225E-04 2.1784306E-02 at 50iterations finished qdiffx linear iterations at : 14:13:48 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 1.4171225E-04 2.1784306E-02 energy calculations done at 3.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 14:13:48 3.738u 0.197s 0:04.26 92.0% 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 15 2011 at 14:13:49 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4581 !!! WARNING: HEM 810 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.568236 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): -24.71100 40.01300 ymin,ymax (A): -18.17800 46.73200 zmin,zma (A): 7.104001 75.20600 x,y,z range (A): 64.72400 64.91000 68.10200 scale (grids/A): 1.568236 object centre (A): 7.651000 14.27700 41.15500 number of atom coordinates read : 4581 total number of charged atoms : 4341 net assigned charge : 7.800027 assigned positive charge : 695.0057 centred at (gu) : 94.17648 86.83114 83.13879 assigned negative charge : -687.2094 centred at (gu) : 94.49512 87.14671 82.72887 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 91134 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41631 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 26895 mr = 61781 m= 2432 mr = 17908 m= 44 mr = 1009 m= 0 mr = 2 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 302 time to turn everything in is 0.4900000 number of dielectric boundary points 39805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 497 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 32925 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) : 0.5227453 object centre at (A) : 7.651000 14.27700 41.15500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1164408E-03 2.2578461E-02 midg,1,midg; midg,igrid,midg 4.9329102E-03 -8.8019669E-03 1,midg,midg; igrid,midg,midg 1.2567006E-02 2.9658969E-03 gauss-seidel spectral radius is 0.9981947 estimated iterations to convergence 187 setup time was (sec) 0.8200000 now iterating at: 14:13:50 rms-change max change #iterations 3.943060 168.9428 at 10iterations 1.649845 66.02686 at 20iterations 0.6883421 23.52737 at 30iterations 0.2891397 10.32642 at 40iterations 0.1203973 3.692046 at 50iterations 5.0682638E-02 1.551160 at 60iterations 2.1304190E-02 0.6384583 at 70iterations 9.0623721E-03 0.3111467 at 80iterations 3.9327489E-03 0.1294518 at 90iterations 1.8366569E-03 6.4929962E-02 at 100iterations 9.6400233E-04 3.5892487E-02 at 110iterations 5.9303048E-04 2.0092010E-02 at 120iterations finished qdiffx linear iterations at : 14:13:59 total time elapsed so far: 9.250000 # loops : 120 mean,max change (kT/e) : 5.9303048E-04 2.0092010E-02 energy calculations done at 9.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.380000 DelPhi exited at 14:14:00 9.381u 0.359s 0:11.14 87.3% 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 15 2011 at 14:14:00 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4581 !!! WARNING: HEM 810 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.352354 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): -24.71100 40.01300 ymin,ymax (A): -18.17800 46.73200 zmin,zma (A): 7.104001 75.20600 x,y,z range (A): 64.72400 64.91000 68.10200 scale (grids/A): 2.352354 object centre (A): 7.651000 14.27700 41.15500 number of atom coordinates read : 4581 total number of charged atoms : 4341 net assigned charge : 7.800027 assigned positive charge : 695.0057 centred at (gu) : 96.26449 85.24643 79.70794 assigned negative charge : -687.2094 centred at (gu) : 96.74249 85.72000 79.09314 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 212013 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41631 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 95633 mr = 152100 m= 24577 mr = 74295 m= 3534 mr = 17621 m= 231 mr = 2174 m= 2 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 983 time to turn everything in is 1.090000 number of dielectric boundary points 89712 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 34671 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) : 1.568236 object centre at (A) : 7.651000 14.27700 41.15500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4859210 0.5159125 midg,1,midg; midg,igrid,midg 1.1176429E-02 -0.1880435 1,midg,midg; igrid,midg,midg 0.2015534 7.7314287E-02 gauss-seidel spectral radius is 0.9991831 estimated iterations to convergence 276 setup time was (sec) 1.350000 now iterating at: 14:14:01 rms-change max change #iterations 10.47553 261.4749 at 10iterations 6.032725 165.8573 at 20iterations 3.455330 70.83861 at 30iterations 1.965631 43.79430 at 40iterations 1.113242 27.90903 at 50iterations 0.6295564 14.83633 at 60iterations 0.3548231 7.363704 at 70iterations 0.2000277 4.137589 at 80iterations 0.1124628 2.210515 at 90iterations 6.3165531E-02 1.248857 at 100iterations 3.5539854E-02 0.7575645 at 110iterations 1.9943152E-02 0.3796577 at 120iterations 1.1165882E-02 0.1972849 at 130iterations 6.2575652E-03 0.1202393 at 140iterations 3.5205444E-03 6.6874504E-02 at 150iterations 1.9768090E-03 4.0609360E-02 at 160iterations 1.1165163E-03 2.1305084E-02 at 170iterations 6.3742569E-04 1.2207031E-02 at 180iterations finished qdiffx linear iterations at : 14:14:14 total time elapsed so far: 13.72000 # loops : 180 mean,max change (kT/e) : 6.3742569E-04 1.2207031E-02 energy calculations done at 13.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.86000 DelPhi exited at 14:14:14 13.859u 0.267s 0:14.45 97.6% 0+0k 0+0io 0pf+0w