Mon Oct 10 17:08:43 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 17:08:44 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2683 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: 0.5448591 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): -2.650000 41.26500 ymin,ymax (A): -10.03300 42.68800 zmin,zma (A): -2.500000 62.83800 x,y,z range (A): 43.91500 52.72100 65.33800 scale (grids/A): 0.5448591 object centre (A): 19.30750 16.32750 30.16900 number of atom coordinates read : 2683 total number of charged atoms : 2545 net assigned charge : 7.000025 assigned positive charge : 398.7726 centred at (gu) : 89.41577 89.45872 89.39660 assigned negative charge : -391.7736 centred at (gu) : 89.45475 89.37429 89.48905 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5191 nv = 96 ne = 84 npr = 53222 no. pairs analyzed = 53222 no. exposed pairs = 3658 no. arc points = 26138 no. surface atoms = 1224 nbur = 1459 mkacc time = 9.0000004E-02 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 = 1.568000 m= 192 mr = 2476 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2627 ## 363 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6812 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0781298E-09 -9.1785725E-11 midg,1,midg; midg,igrid,midg -7.6241437E-11 7.7408041E-10 1,midg,midg; igrid,midg,midg 7.3066792E-10 1.7118219E-10 gauss-seidel spectral radius is 0.9826163 estimated iterations to convergence 62 setup time was (sec) 0.3800000 now iterating at: 17:08:44 rms-change max change #iterations 6.6941366E-02 12.71693 at 10iterations 4.4271471E-03 0.7237287 at 20iterations 3.3781782E-04 5.6823730E-02 at 30iterations 3.8288439E-05 6.8569183E-03 at 40iterations 6.5496843E-06 1.3113022E-03 at 50iterations finished qdiffx linear iterations at : 17:08:47 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 6.5496843E-06 1.3113022E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 17:08:47 3.396u 0.180s 0:03.98 89.6% 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 17:08:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2683 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: 1.634577 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): -2.650000 41.26500 ymin,ymax (A): -10.03300 42.68800 zmin,zma (A): -2.500000 62.83800 x,y,z range (A): 43.91500 52.72100 65.33800 scale (grids/A): 1.634577 object centre (A): 19.30750 16.32750 30.16900 number of atom coordinates read : 2683 total number of charged atoms : 2545 net assigned charge : 7.000025 assigned positive charge : 398.7726 centred at (gu) : 88.24683 88.37580 88.18913 assigned negative charge : -391.7736 centred at (gu) : 88.36386 88.12249 88.46729 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 57515 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26138 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 16677 mr = 37205 m= 1714 mr = 10842 m= 51 mr = 787 m= 0 mr = 2 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 205 time to turn everything in is 0.2800000 number of dielectric boundary points 27121 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 342 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 19505 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) : 0.5448591 object centre at (A) : 19.30750 16.32750 30.16900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3828657E-02 1.6677190E-02 midg,1,midg; midg,igrid,midg -9.9734534E-03 3.2439507E-03 1,midg,midg; igrid,midg,midg 7.7189617E-03 1.3269614E-03 gauss-seidel spectral radius is 0.9981640 estimated iterations to convergence 185 setup time was (sec) 0.4900000 now iterating at: 17:08:48 rms-change max change #iterations 3.120783 169.4781 at 10iterations 1.287927 55.32108 at 20iterations 0.5345424 21.52695 at 30iterations 0.2215601 8.347345 at 40iterations 9.1616094E-02 3.486252 at 50iterations 3.8050324E-02 1.589132 at 60iterations 1.5772913E-02 0.5758972 at 70iterations 6.5834792E-03 0.2617331 at 80iterations 2.7413908E-03 0.1091385 at 90iterations 1.1434803E-03 4.5011520E-02 at 100iterations 4.7987176E-04 1.8439293E-02 at 110iterations 2.0359059E-04 7.6780319E-03 at 120iterations finished qdiffx linear iterations at : 17:08:55 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 2.0359059E-04 7.6780319E-03 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 17:08:56 7.575u 0.211s 0:08.18 95.1% 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 17:08:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2683 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: 2.451866 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): -2.650000 41.26500 ymin,ymax (A): -10.03300 42.68800 zmin,zma (A): -2.500000 62.83800 x,y,z range (A): 43.91500 52.72100 65.33800 scale (grids/A): 2.451866 object centre (A): 19.30750 16.32750 30.16900 number of atom coordinates read : 2683 total number of charged atoms : 2545 net assigned charge : 7.000025 assigned positive charge : 398.7726 centred at (gu) : 87.37009 87.56350 87.28364 assigned negative charge : -391.7736 centred at (gu) : 87.54579 87.18365 87.70097 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 133568 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26138 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 58391 mr = 91639 m= 15706 mr = 44564 m= 2521 mr = 11312 m= 189 mr = 1576 m= 6 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 646 time to turn everything in is 0.6800000 number of dielectric boundary points 61212 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20327 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) : 1.634577 object centre at (A) : 19.30750 16.32750 30.16900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3364313 0.4179728 midg,1,midg; midg,igrid,midg -0.1148185 5.5718344E-02 1,midg,midg; igrid,midg,midg 0.1039673 1.4734094E-02 gauss-seidel spectral radius is 0.9991308 estimated iterations to convergence 268 setup time was (sec) 0.8900000 now iterating at: 17:08:57 rms-change max change #iterations 8.211966 395.9216 at 10iterations 4.626801 147.3386 at 20iterations 2.596512 68.50351 at 30iterations 1.443046 40.15245 at 40iterations 0.8011696 21.55902 at 50iterations 0.4413125 11.55692 at 60iterations 0.2439603 5.852375 at 70iterations 0.1343264 3.239454 at 80iterations 7.3789418E-02 1.709177 at 90iterations 4.0572949E-02 0.9591351 at 100iterations 2.2233240E-02 0.5004182 at 110iterations 1.2244531E-02 0.2771301 at 120iterations 6.7095221E-03 0.1486259 at 130iterations 3.6791912E-03 8.3898544E-02 at 140iterations 2.0131490E-03 4.6260834E-02 at 150iterations 1.1057844E-03 2.4307251E-02 at 160iterations 6.0620805E-04 1.3061523E-02 at 170iterations 3.3222561E-04 7.4939728E-03 at 180iterations finished qdiffx linear iterations at : 17:09:08 total time elapsed so far: 11.92000 # loops : 180 mean,max change (kT/e) : 3.3222561E-04 7.4939728E-03 energy calculations done at 11.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.05000 DelPhi exited at 17:09:09 12.053u 0.228s 0:13.37 91.7% 0+0k 0+0io 0pf+0w