Mon Oct 10 17:15:20 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 17:15:21 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 = 3019 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: 0.5429230 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): -31.16500 34.40600 ymin,ymax (A): -25.89300 26.38600 zmin,zma (A): -42.38900 6.377000 x,y,z range (A): 65.57100 52.27900 48.76600 scale (grids/A): 0.5429230 object centre (A): 1.620502 0.2465000 -18.00600 number of atom coordinates read : 3019 total number of charged atoms : 2877 net assigned charge : -4.499966 assigned positive charge : 453.5008 centred at (gu) : 90.50646 88.56789 91.30312 assigned negative charge : -458.0021 centred at (gu) : 90.53897 88.74789 91.42336 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5755 nv = 96 ne = 84 npr = 60051 no. pairs analyzed = 60051 no. exposed pairs = 4054 no. arc points = 28096 no. surface atoms = 1363 nbur = 1656 mkacc time = 0.1300000 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= 226 mr = 2845 m= 0 mr = 10 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3126 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2870 ## 357 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7614 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3482667E-10 -1.3800301E-09 midg,1,midg; midg,igrid,midg 1.1840381E-09 -9.5933583E-10 1,midg,midg; igrid,midg,midg -4.9505431E-11 -5.0988769E-10 gauss-seidel spectral radius is 0.9825189 estimated iterations to convergence 62 setup time was (sec) 0.6200000 now iterating at: 17:15:21 rms-change max change #iterations 6.9954082E-02 11.98031 at 10iterations 4.6460084E-03 0.9691718 at 20iterations 2.9972455E-04 4.8409462E-02 at 30iterations 2.0147621E-05 4.0307045E-03 at 40iterations 1.4058272E-06 2.2888184E-04 at 50iterations finished qdiffx linear iterations at : 17:15:25 total time elapsed so far: 4.190000 # loops : 50 mean,max change (kT/e) : 1.4058272E-06 2.2888184E-04 energy calculations done at 4.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.360000 DelPhi exited at 17:15:26 4.366u 0.267s 0:05.01 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 Mon Oct 10 2011 at 17:15:26 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 = 3019 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: 1.628769 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): -31.16500 34.40600 ymin,ymax (A): -25.89300 26.38600 zmin,zma (A): -42.38900 6.377000 x,y,z range (A): 65.57100 52.27900 48.76600 scale (grids/A): 1.628769 object centre (A): 1.620502 0.2465000 -18.00600 number of atom coordinates read : 3019 total number of charged atoms : 2877 net assigned charge : -4.499966 assigned positive charge : 453.5008 centred at (gu) : 91.51839 85.70290 93.90872 assigned negative charge : -458.0021 centred at (gu) : 91.61668 86.24317 94.26989 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 63617 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28096 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 17946 mr = 41647 m= 1621 mr = 11920 m= 42 mr = 709 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 736 time to turn everything in is 0.4800000 number of dielectric boundary points 28942 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 319 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 21984 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) : 0.5429230 object centre at (A) : 1.620502 0.2465000 -18.00600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9063790E-03 -8.6787995E-03 midg,1,midg; midg,igrid,midg 1.2221646E-02 -1.2633761E-02 1,midg,midg; igrid,midg,midg -8.9805741E-05 -2.5606442E-02 gauss-seidel spectral radius is 0.9981774 estimated iterations to convergence 186 setup time was (sec) 0.8100000 now iterating at: 17:15:27 rms-change max change #iterations 3.327658 174.5269 at 10iterations 1.375473 57.60647 at 20iterations 0.5712605 26.61597 at 30iterations 0.2372078 10.40854 at 40iterations 9.8564595E-02 3.435784 at 50iterations 4.0990770E-02 1.459955 at 60iterations 1.6950987E-02 0.6416016 at 70iterations 7.0711584E-03 0.2486687 at 80iterations 2.9420881E-03 0.1007309 at 90iterations 1.2226366E-03 4.3803930E-02 at 100iterations 5.0797581E-04 1.7486572E-02 at 110iterations 2.1226388E-04 8.0518723E-03 at 120iterations finished qdiffx linear iterations at : 17:15:35 total time elapsed so far: 9.230000 # loops : 120 mean,max change (kT/e) : 2.1226388E-04 8.0518723E-03 energy calculations done at 9.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.400000 DelPhi exited at 17:15:36 9.404u 0.237s 0:09.98 96.4% 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 17:15:36 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 = 3019 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: 2.443153 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): -31.16500 34.40600 ymin,ymax (A): -25.89300 26.38600 zmin,zma (A): -42.38900 6.377000 x,y,z range (A): 65.57100 52.27900 48.76600 scale (grids/A): 2.443153 object centre (A): 1.620502 0.2465000 -18.00600 number of atom coordinates read : 3019 total number of charged atoms : 2877 net assigned charge : -4.499966 assigned positive charge : 453.5008 centred at (gu) : 92.27718 83.55400 95.86261 assigned negative charge : -458.0021 centred at (gu) : 92.42497 84.36471 96.40469 start vw surface at 0.1700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 148078 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28096 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 63808 mr = 102856 m= 16592 mr = 49244 m= 2353 mr = 12059 m= 138 mr = 1428 m= 0 mr = 63 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 2532 time to turn everything in is 1.180000 number of dielectric boundary points 65319 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 22984 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) : 1.628769 object centre at (A) : 1.620502 0.2465000 -18.00600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5153453E-02 -9.6744724E-02 midg,1,midg; midg,igrid,midg 0.2022273 -0.1800637 1,midg,midg; igrid,midg,midg 5.3691939E-02 -0.7520990 gauss-seidel spectral radius is 0.9991406 estimated iterations to convergence 269 setup time was (sec) 1.520000 now iterating at: 17:15:37 rms-change max change #iterations 8.731853 270.5687 at 10iterations 4.891305 145.5159 at 20iterations 2.730890 61.08526 at 30iterations 1.516741 34.02965 at 40iterations 0.8411728 23.16167 at 50iterations 0.4642902 9.527107 at 60iterations 0.2561156 6.090185 at 70iterations 0.1410428 2.768490 at 80iterations 7.7691734E-02 1.643326 at 90iterations 4.2706043E-02 0.9481434 at 100iterations 2.3495266E-02 0.4755154 at 110iterations 1.2900062E-02 0.2499743 at 120iterations 7.0914985E-03 0.1443481 at 130iterations 3.9003559E-03 7.8666687E-02 at 140iterations 2.1392659E-03 4.2740345E-02 at 150iterations 1.1749391E-03 2.3517609E-02 at 160iterations 6.4553530E-04 1.3810158E-02 at 170iterations 3.5507043E-04 7.0482492E-03 at 180iterations finished qdiffx linear iterations at : 17:15:51 total time elapsed so far: 14.78000 # loops : 180 mean,max change (kT/e) : 3.5507043E-04 7.0482492E-03 energy calculations done at 14.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.96000 DelPhi exited at 17:15:51 14.963u 0.276s 0:15.60 97.6% 0+0k 0+0io 0pf+0w