Mon Oct 10 11:33:35 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 11:33:35 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2138 !!! WARNING: ASL 51 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7207645 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): -10.88400 38.39200 ymin,ymax (A): -22.12800 26.83200 zmin,zma (A): -13.22500 36.16700 x,y,z range (A): 49.27600 48.96000 49.39200 scale (grids/A): 0.7207645 object centre (A): 13.75400 2.351999 11.47100 number of atom coordinates read : 2138 total number of charged atoms : 1998 net assigned charge : -6.099981 assigned positive charge : 324.2838 centred at (gu) : 88.13371 88.43275 89.76598 assigned negative charge : -330.3839 centred at (gu) : 87.96407 88.35870 89.95109 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7624 nv = 96 ne = 84 npr = 44043 no. pairs analyzed = 44043 no. exposed pairs = 2730 no. arc points = 19106 no. surface atoms = 920 nbur = 1218 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 523 mr = 4241 m= 5 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 185 time to turn everything in is 0.1800000 number of dielectric boundary points 3822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1622 ## 112 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8197 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3184771E-08 -1.8895138E-07 midg,1,midg; midg,igrid,midg -1.5970852E-07 -1.2168069E-08 1,midg,midg; igrid,midg,midg -2.6806816E-07 3.3590489E-08 gauss-seidel spectral radius is 0.9899753 estimated iterations to convergence 81 setup time was (sec) 0.3700000 now iterating at: 11:33:36 rms-change max change #iterations 0.2254511 27.47578 at 10iterations 2.8665343E-02 3.587341 at 20iterations 3.6306954E-03 0.4780598 at 30iterations 4.6519178E-04 6.2450409E-02 at 40iterations 5.9222439E-05 8.3084106E-03 at 50iterations finished qdiffx linear iterations at : 11:33:39 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 5.9222439E-05 8.3084106E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 11:33:39 3.370u 0.168s 0:03.81 92.6% 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 11:33:39 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2138 !!! WARNING: ASL 51 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.162294 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): -10.88400 38.39200 ymin,ymax (A): -22.12800 26.83200 zmin,zma (A): -13.22500 36.16700 x,y,z range (A): 49.27600 48.96000 49.39200 scale (grids/A): 2.162294 object centre (A): 13.75400 2.351999 11.47100 number of atom coordinates read : 2138 total number of charged atoms : 1998 net assigned charge : -6.099981 assigned positive charge : 324.2838 centred at (gu) : 84.40073 85.29819 89.29776 assigned negative charge : -330.3839 centred at (gu) : 83.89207 85.07603 89.85325 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 80425 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19106 grid for indexing accessible points = 1.400000 m= 31252 mr = 55289 m= 6187 mr = 23595 m= 588 mr = 4124 m= 12 mr = 264 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 4759 time to turn everything in is 0.4200000 number of dielectric boundary points 35192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 15891 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) : 0.7207645 object centre at (A) : 13.75400 2.351999 11.47100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.9050393E-03 -7.8163981E-02 midg,1,midg; midg,igrid,midg -1.9211758E-02 8.7833395E-03 1,midg,midg; igrid,midg,midg -6.1538897E-02 2.8712902E-02 gauss-seidel spectral radius is 0.9988779 estimated iterations to convergence 236 setup time was (sec) 0.6400000 now iterating at: 11:33:40 rms-change max change #iterations 4.977039 182.0582 at 10iterations 2.491741 91.83516 at 20iterations 1.247050 37.13201 at 30iterations 0.6260611 19.37902 at 40iterations 0.3156220 9.401882 at 50iterations 0.1579529 4.673931 at 60iterations 7.9186067E-02 2.285789 at 70iterations 3.9916869E-02 1.169761 at 80iterations 2.0018928E-02 0.5453033 at 90iterations 1.0053118E-02 0.3091593 at 100iterations 5.0495644E-03 0.1542805 at 110iterations 2.5344945E-03 7.0817947E-02 at 120iterations finished qdiffx linear iterations at : 11:33:47 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 2.5344945E-03 7.0817947E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 11:33:48 7.918u 0.177s 0:08.58 94.1% 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 11:33:48 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2138 !!! WARNING: ASL 51 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.243440 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): -10.88400 38.39200 ymin,ymax (A): -22.12800 26.83200 zmin,zma (A): -13.22500 36.16700 x,y,z range (A): 49.27600 48.96000 49.39200 scale (grids/A): 3.243440 object centre (A): 13.75400 2.351999 11.47100 number of atom coordinates read : 2138 total number of charged atoms : 1998 net assigned charge : -6.099981 assigned positive charge : 324.2838 centred at (gu) : 81.60104 82.94723 88.94659 assigned negative charge : -330.3839 centred at (gu) : 80.83807 82.61406 89.77985 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 185116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19106 grid for indexing accessible points = 1.400000 m= 97158 mr = 133294 m= 39856 mr = 80374 m= 11741 mr = 32707 m= 2495 mr = 9132 m= 259 mr = 1803 m= 8 mr = 102 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 16089 time to turn everything in is 1.230000 number of dielectric boundary points 79221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 15984 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) : 2.162294 object centre at (A) : 13.75400 2.351999 11.47100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1133212E-02 -0.6058283 midg,1,midg; midg,igrid,midg -7.0440739E-02 -1.4010438E-02 1,midg,midg; igrid,midg,midg -0.4665489 0.1859670 gauss-seidel spectral radius is 0.9993133 estimated iterations to convergence 301 setup time was (sec) 1.450000 now iterating at: 11:33:50 rms-change max change #iterations 10.92383 486.7664 at 10iterations 6.454123 134.6582 at 20iterations 3.777537 79.26736 at 30iterations 2.224759 44.21862 at 40iterations 1.304134 24.58108 at 50iterations 0.7665154 13.13881 at 60iterations 0.4504161 7.967148 at 70iterations 0.2634578 4.455465 at 80iterations 0.1547086 2.837387 at 90iterations 9.0597756E-02 1.491778 at 100iterations 5.3112000E-02 0.9026337 at 110iterations 3.1115809E-02 0.5265980 at 120iterations 1.8273557E-02 0.3168488 at 130iterations 1.0686548E-02 0.2022095 at 140iterations 6.2726531E-03 0.1113663 at 150iterations 3.6692608E-03 6.2419891E-02 at 160iterations 2.1529489E-03 3.6823273E-02 at 170iterations 1.2606366E-03 2.1163940E-02 at 180iterations finished qdiffx linear iterations at : 11:34:01 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 1.2606366E-03 2.1163940E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 11:34:01 13.091u 0.219s 0:13.58 97.9% 0+0k 0+0io 0pf+0w