Tue Oct 11 08:22:48 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 Tue Oct 11 2011 at 08:22:48 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 = 2547 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5638264 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): 17.82900 80.96900 ymin,ymax (A): -13.08000 39.56800 zmin,zma (A): -8.150000 34.62500 x,y,z range (A): 63.14000 52.64800 42.77500 scale (grids/A): 0.5638264 object centre (A): 49.39900 13.24400 13.23750 number of atom coordinates read : 2547 total number of charged atoms : 2408 net assigned charge : 8.500027 assigned positive charge : 381.2379 centred at (gu) : 87.57790 91.10014 89.97330 assigned negative charge : -372.7385 centred at (gu) : 87.76317 91.21014 90.07365 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5191 nv = 96 ne = 84 npr = 51124 no. pairs analyzed = 51124 no. exposed pairs = 3016 no. arc points = 21057 no. surface atoms = 1025 nbur = 1522 mkacc time = 0.1100000 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 = 1.540000 m= 227 mr = 2856 m= 0 mr = 20 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3100000 number of dielectric boundary points 2542 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2107 ## 258 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6745 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0559672E-09 -7.4264518E-11 midg,1,midg; midg,igrid,midg 1.6500806E-09 -2.5328040E-10 1,midg,midg; igrid,midg,midg 5.2494720E-09 -5.4244176E-10 gauss-seidel spectral radius is 0.9837340 estimated iterations to convergence 64 setup time was (sec) 0.5200000 now iterating at: 08:22:49 rms-change max change #iterations 8.1022598E-02 13.52290 at 10iterations 7.2566746E-03 1.347755 at 20iterations 1.0033898E-03 0.2524338 at 30iterations 2.5202770E-04 6.8523407E-02 at 40iterations 6.9655303E-05 1.8810272E-02 at 50iterations finished qdiffx linear iterations at : 08:22:51 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 6.9655303E-05 1.8810272E-02 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 08:22:52 3.172u 0.151s 0:03.68 90.2% 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 Tue Oct 11 2011 at 08:22:52 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 = 2547 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: 1.691479 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): 17.82900 80.96900 ymin,ymax (A): -13.08000 39.56800 zmin,zma (A): -8.150000 34.62500 x,y,z range (A): 63.14000 52.64800 42.77500 scale (grids/A): 1.691479 object centre (A): 49.39900 13.24400 13.23750 number of atom coordinates read : 2547 total number of charged atoms : 2408 net assigned charge : 8.500027 assigned positive charge : 381.2379 centred at (gu) : 82.73328 93.29987 89.91920 assigned negative charge : -372.7385 centred at (gu) : 83.28938 93.63021 90.22066 start vw surface at 0.1900000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 57812 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21057 grid for indexing accessible points = 1.400000 m= 19534 mr = 40162 m= 2442 mr = 14445 m= 63 mr = 1433 m= 0 mr = 4 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 712 time to turn everything in is 0.4600000 number of dielectric boundary points 23807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 18546 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) : 0.5638264 object centre at (A) : 49.39900 13.24400 13.23750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3822233E-02 2.4381238E-03 midg,1,midg; midg,igrid,midg 1.1192715E-02 8.5223801E-03 1,midg,midg; igrid,midg,midg 3.6996804E-04 6.2455763E-03 gauss-seidel spectral radius is 0.9982576 estimated iterations to convergence 190 setup time was (sec) 0.7100000 now iterating at: 08:22:53 rms-change max change #iterations 3.248837 134.6619 at 10iterations 1.377687 53.21704 at 20iterations 0.5866240 24.54760 at 30iterations 0.2498662 8.879879 at 40iterations 0.1066565 3.761333 at 50iterations 4.5585807E-02 1.675247 at 60iterations 1.9473553E-02 0.7234316 at 70iterations 8.4383897E-03 0.3635998 at 80iterations 3.7396720E-03 0.1382771 at 90iterations 1.7413868E-03 7.2231293E-02 at 100iterations 8.5543591E-04 3.8539886E-02 at 110iterations 4.4926931E-04 2.3666382E-02 at 120iterations finished qdiffx linear iterations at : 08:22:59 total time elapsed so far: 7.190000 # loops : 120 mean,max change (kT/e) : 4.4926931E-04 2.3666382E-02 energy calculations done at 7.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.360000 DelPhi exited at 08:23:00 7.363u 0.163s 0:07.88 95.4% 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 Tue Oct 11 2011 at 08:23:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2547 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: 2.537219 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): 17.82900 80.96900 ymin,ymax (A): -13.08000 39.56800 zmin,zma (A): -8.150000 34.62500 x,y,z range (A): 63.14000 52.64800 42.77500 scale (grids/A): 2.537219 object centre (A): 49.39900 13.24400 13.23750 number of atom coordinates read : 2547 total number of charged atoms : 2408 net assigned charge : 8.500027 assigned positive charge : 381.2379 centred at (gu) : 79.09966 94.94986 89.87872 assigned negative charge : -372.7385 centred at (gu) : 79.93395 95.44526 90.33092 start vw surface at 0.1500000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 134112 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21057 grid for indexing accessible points = 1.400000 m= 65100 mr = 97459 m= 21323 mr = 53342 m= 4009 mr = 17223 m= 338 mr = 2999 m= 3 mr = 176 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 2464 time to turn everything in is 0.9900000 number of dielectric boundary points 53686 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 19256 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) : 1.691479 object centre at (A) : 49.39900 13.24400 13.23750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1681287 3.6568910E-02 midg,1,midg; midg,igrid,midg 0.1193157 0.1776597 1,midg,midg; igrid,midg,midg -0.2430636 9.1873348E-02 gauss-seidel spectral radius is 0.9991423 estimated iterations to convergence 270 setup time was (sec) 1.260000 now iterating at: 08:23:01 rms-change max change #iterations 8.079951 286.5093 at 10iterations 4.449259 128.9937 at 20iterations 2.460557 56.30387 at 30iterations 1.349673 28.88405 at 40iterations 0.7439035 15.67258 at 50iterations 0.4097753 9.171985 at 60iterations 0.2258299 4.899193 at 70iterations 0.1240018 2.702802 at 80iterations 6.8196476E-02 1.588339 at 90iterations 3.7648756E-02 0.8930664 at 100iterations 2.0812500E-02 0.4284267 at 110iterations 1.1530144E-02 0.2651176 at 120iterations 6.4514587E-03 0.1414185 at 130iterations 3.6743621E-03 9.4436646E-02 at 140iterations 2.1539265E-03 5.3764343E-02 at 150iterations 1.3057914E-03 3.6300659E-02 at 160iterations 8.2927191E-04 2.4532318E-02 at 170iterations 5.5372110E-04 1.6544342E-02 at 180iterations finished qdiffx linear iterations at : 08:23:10 total time elapsed so far: 10.42000 # loops : 180 mean,max change (kT/e) : 5.5372110E-04 1.6544342E-02 energy calculations done at 10.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.60000 DelPhi exited at 08:23:11 10.604u 0.171s 0:11.30 95.3% 0+0k 0+0io 0pf+0w