Mon Oct 10 09:53:42 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 Mon Oct 10 2011 at 09:53:42 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2786 !!! WARNING: HIT 225 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5852857 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): -17.47800 36.12100 ymin,ymax (A): -63.38700 -4.780000 zmin,zma (A): -4.338000 56.48700 x,y,z range (A): 53.59900 58.60700 60.82500 scale (grids/A): 0.5852857 object centre (A): 9.321499 -34.08350 26.07450 number of atom coordinates read : 2786 total number of charged atoms : 2633 net assigned charge : 4.014013 assigned positive charge : 407.0860 centred at (gu) : 89.01933 89.29623 87.31283 assigned negative charge : -403.0724 centred at (gu) : 89.14560 89.19538 87.18737 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6453 nv = 96 ne = 84 npr = 54306 no. pairs analyzed = 54306 no. exposed pairs = 4297 no. arc points = 30838 no. surface atoms = 1406 nbur = 1380 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 = 1.484000 m= 317 mr = 2804 m= 2 mr = 13 m= 0 mr = 0 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 3955 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2955 ## 311 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8010 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6306096E-09 2.1722815E-09 midg,1,midg; midg,igrid,midg -1.5163190E-09 2.9410163E-09 1,midg,midg; igrid,midg,midg 5.0895035E-09 -1.4889873E-09 gauss-seidel spectral radius is 0.9849321 estimated iterations to convergence 67 setup time was (sec) 0.5700000 now iterating at: 09:53:42 rms-change max change #iterations 9.5502719E-02 18.07607 at 10iterations 7.6053152E-03 1.225326 at 20iterations 6.2225026E-04 9.3468666E-02 at 30iterations 5.6953908E-05 8.0204010E-03 at 40iterations 8.4818012E-06 1.0614395E-03 at 50iterations finished qdiffx linear iterations at : 09:53:45 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 8.4818012E-06 1.0614395E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 09:53:48 3.622u 0.214s 0:05.82 65.8% 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 Mon Oct 10 2011 at 09:53:48 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2786 !!! WARNING: HIT 225 has a net charge of 0.5140 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: 1.755857 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): -17.47800 36.12100 ymin,ymax (A): -63.38700 -4.780000 zmin,zma (A): -4.338000 56.48700 x,y,z range (A): 53.59900 58.60700 60.82500 scale (grids/A): 1.755857 object centre (A): 9.321499 -34.08350 26.07450 number of atom coordinates read : 2786 total number of charged atoms : 2633 net assigned charge : 4.014013 assigned positive charge : 407.0860 centred at (gu) : 87.05746 87.88813 81.93807 assigned negative charge : -403.0724 centred at (gu) : 87.43636 87.58602 81.56176 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 68521 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30838 grid for indexing accessible points = 1.400000 m= 21681 mr = 41702 m= 2800 mr = 13552 m= 103 mr = 1200 m= 3 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 36643 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 243 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 20490 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) : 0.5852857 object centre at (A) : 9.321499 -34.08350 26.07450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2608256E-02 3.7349877E-03 midg,1,midg; midg,igrid,midg 1.2388525E-02 3.1427778E-02 1,midg,midg; igrid,midg,midg 2.1861793E-02 4.9322522E-03 gauss-seidel spectral radius is 0.9984369 estimated iterations to convergence 201 setup time was (sec) 0.9200000 now iterating at: 09:53:49 rms-change max change #iterations 3.708780 177.3564 at 10iterations 1.640727 61.93532 at 20iterations 0.7299578 26.13719 at 30iterations 0.3218062 11.26017 at 40iterations 0.1428856 5.015060 at 50iterations 6.3303933E-02 2.276317 at 60iterations 2.8116276E-02 1.006715 at 70iterations 1.2463710E-02 0.4175491 at 80iterations 5.5430704E-03 0.1952820 at 90iterations 2.4568769E-03 8.6661220E-02 at 100iterations 1.0911482E-03 4.5475006E-02 at 110iterations 4.8363552E-04 1.6260862E-02 at 120iterations finished qdiffx linear iterations at : 09:53:56 total time elapsed so far: 8.140000 # loops : 120 mean,max change (kT/e) : 4.8363552E-04 1.6260862E-02 energy calculations done at 8.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.330000 DelPhi exited at 09:53:56 8.333u 0.204s 0:08.81 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 Mon Oct 10 2011 at 09:53:56 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2786 !!! WARNING: HIT 225 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.633785 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): -17.47800 36.12100 ymin,ymax (A): -63.38700 -4.780000 zmin,zma (A): -4.338000 56.48700 x,y,z range (A): 53.59900 58.60700 60.82500 scale (grids/A): 2.633785 object centre (A): 9.321499 -34.08350 26.07450 number of atom coordinates read : 2786 total number of charged atoms : 2633 net assigned charge : 4.014013 assigned positive charge : 407.0860 centred at (gu) : 85.58606 86.83218 77.90724 assigned negative charge : -403.0724 centred at (gu) : 86.15441 86.37883 77.34266 start vw surface at 0.1900000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 158361 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30838 grid for indexing accessible points = 1.400000 m= 70953 mr = 103104 m= 22981 mr = 52559 m= 4451 mr = 16214 m= 390 mr = 2519 m= 12 mr = 160 m= 0 mr = 0 time to grow re-entrant surface = 0.7500001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.370000 number of dielectric boundary points 82592 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 21052 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) : 1.755857 object centre at (A) : 9.321499 -34.08350 26.07450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3310016 3.2179769E-02 midg,1,midg; midg,igrid,midg 0.4546053 0.4354197 1,midg,midg; igrid,midg,midg 0.1931370 9.0672761E-02 gauss-seidel spectral radius is 0.9992340 estimated iterations to convergence 285 setup time was (sec) 1.720000 now iterating at: 09:53:58 rms-change max change #iterations 9.424175 326.0613 at 10iterations 5.584622 154.1030 at 20iterations 3.266530 83.41081 at 30iterations 1.897788 46.06406 at 40iterations 1.096059 27.25363 at 50iterations 0.6314467 14.59398 at 60iterations 0.3634528 9.443737 at 70iterations 0.2083438 5.061912 at 80iterations 0.1192694 2.742879 at 90iterations 6.8273373E-02 1.562336 at 100iterations 3.9094113E-02 0.9030685 at 110iterations 2.2294743E-02 0.4893627 at 120iterations 1.2749770E-02 0.2554979 at 130iterations 7.2604343E-03 0.1484909 at 140iterations 4.1368050E-03 8.9538574E-02 at 150iterations 2.3641326E-03 5.0650835E-02 at 160iterations 1.3436232E-03 2.7307510E-02 at 170iterations 7.6456176E-04 1.6849518E-02 at 180iterations finished qdiffx linear iterations at : 09:54:10 total time elapsed so far: 13.29000 # loops : 180 mean,max change (kT/e) : 7.6456176E-04 1.6849518E-02 energy calculations done at 13.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.48000 DelPhi exited at 09:54:10 13.481u 0.235s 0:13.97 98.1% 0+0k 0+0io 0pf+0w