Mon Oct 10 23:51:56 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 23:51:57 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 = 2623 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: 0.5883228 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): 10.06800 64.70900 ymin,ymax (A): -1.242000 59.26900 zmin,zma (A): 10.18300 53.97600 x,y,z range (A): 54.64100 60.51100 43.79300 scale (grids/A): 0.5883228 object centre (A): 37.38850 29.01350 32.07950 number of atom coordinates read : 2623 total number of charged atoms : 2483 net assigned charge : 9.000021 assigned positive charge : 394.9107 centred at (gu) : 88.77115 90.70600 89.57784 assigned negative charge : -385.9114 centred at (gu) : 88.77950 90.59197 89.70084 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5928 nv = 96 ne = 84 npr = 52988 no. pairs analyzed = 52988 no. exposed pairs = 3154 no. arc points = 21783 no. surface atoms = 1063 nbur = 1560 mkacc time = 8.9999996E-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 = 1.456000 m= 257 mr = 3271 m= 0 mr = 13 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 61 time to turn everything in is 0.2000000 number of dielectric boundary points 2901 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2226 ## 250 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7471 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1850169E-09 -4.8707438E-10 midg,1,midg; midg,igrid,midg -2.5246033E-10 6.3467898E-09 1,midg,midg; igrid,midg,midg 3.6752681E-09 1.8032831E-09 gauss-seidel spectral radius is 0.9850501 estimated iterations to convergence 67 setup time was (sec) 0.3900000 now iterating at: 23:51:57 rms-change max change #iterations 0.1002361 15.50844 at 10iterations 9.3897916E-03 1.424752 at 20iterations 1.2580064E-03 0.2709389 at 30iterations 2.8592165E-04 6.7539215E-02 at 40iterations 7.1206661E-05 1.7364502E-02 at 50iterations finished qdiffx linear iterations at : 23:52:00 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 7.1206661E-05 1.7364502E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 23:52:01 3.506u 0.173s 0:04.43 82.8% 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 23:52:01 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 = 2623 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: 1.764968 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): 10.06800 64.70900 ymin,ymax (A): -1.242000 59.26900 zmin,zma (A): 10.18300 53.97600 x,y,z range (A): 54.64100 60.51100 43.79300 scale (grids/A): 1.764968 object centre (A): 37.38850 29.01350 32.07950 number of atom coordinates read : 2623 total number of charged atoms : 2483 net assigned charge : 9.000021 assigned positive charge : 394.9107 centred at (gu) : 86.31249 92.11749 88.73296 assigned negative charge : -385.9114 centred at (gu) : 86.33834 91.77571 89.10250 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 64823 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21783 grid for indexing accessible points = 1.400000 m= 21671 mr = 45093 m= 2740 mr = 15798 m= 80 mr = 1602 m= 0 mr = 9 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1484 time to turn everything in is 0.3300000 number of dielectric boundary points 26812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 19291 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) : 0.5883228 object centre at (A) : 37.38850 29.01350 32.07950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5223522E-02 4.1983263E-03 midg,1,midg; midg,igrid,midg -1.1903926E-02 -1.2731316E-02 1,midg,midg; igrid,midg,midg 4.2771972E-03 1.3486527E-02 gauss-seidel spectral radius is 0.9984115 estimated iterations to convergence 199 setup time was (sec) 0.5500000 now iterating at: 23:52:02 rms-change max change #iterations 3.618100 157.2526 at 10iterations 1.597402 64.29850 at 20iterations 0.7010490 29.76527 at 30iterations 0.3109925 12.55519 at 40iterations 0.1376690 4.957619 at 50iterations 6.1213117E-02 2.057650 at 60iterations 2.7166333E-02 1.115970 at 70iterations 1.2181062E-02 0.4183979 at 80iterations 5.5687022E-03 0.1910324 at 90iterations 2.6497773E-03 0.1119995 at 100iterations 1.3306389E-03 5.7929993E-02 at 110iterations 7.1865087E-04 3.3748627E-02 at 120iterations finished qdiffx linear iterations at : 23:52:09 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 7.1865087E-04 3.3748627E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 23:52:10 7.959u 0.210s 0:08.71 93.6% 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 23:52:10 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 = 2623 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: 2.647453 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): 10.06800 64.70900 ymin,ymax (A): -1.242000 59.26900 zmin,zma (A): 10.18300 53.97600 x,y,z range (A): 54.64100 60.51100 43.79300 scale (grids/A): 2.647453 object centre (A): 37.38850 29.01350 32.07950 number of atom coordinates read : 2623 total number of charged atoms : 2483 net assigned charge : 9.000021 assigned positive charge : 394.9107 centred at (gu) : 84.46851 93.17612 88.09916 assigned negative charge : -385.9114 centred at (gu) : 84.50744 92.66370 88.65366 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 150511 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21783 grid for indexing accessible points = 1.400000 m= 73067 mr = 109920 m= 23519 mr = 59477 m= 4620 mr = 18598 m= 414 mr = 3338 m= 17 mr = 234 m= 0 mr = 2 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 5394 time to turn everything in is 0.8000000 number of dielectric boundary points 60579 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 19854 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) : 1.764968 object centre at (A) : 37.38850 29.01350 32.07950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3044154 6.3874647E-02 midg,1,midg; midg,igrid,midg -0.3505399 -0.5394015 1,midg,midg; igrid,midg,midg 2.0236776E-03 0.1094645 gauss-seidel spectral radius is 0.9991893 estimated iterations to convergence 277 setup time was (sec) 1.040000 now iterating at: 23:52:11 rms-change max change #iterations 8.781758 357.1896 at 10iterations 4.939141 118.2148 at 20iterations 2.776274 57.38829 at 30iterations 1.560428 35.35299 at 40iterations 0.8735736 17.06432 at 50iterations 0.4876307 10.19160 at 60iterations 0.2745347 5.801745 at 70iterations 0.1537126 3.166076 at 80iterations 8.6077042E-02 1.668030 at 90iterations 4.8156623E-02 1.013466 at 100iterations 2.7029635E-02 0.5243788 at 110iterations 1.5224908E-02 0.3147812 at 120iterations 8.6407987E-03 0.1773114 at 130iterations 4.9496731E-03 0.1010208 at 140iterations 2.8902269E-03 6.5902710E-02 at 150iterations 1.7423499E-03 4.1095734E-02 at 160iterations 1.1048338E-03 2.8450012E-02 at 170iterations 7.3578104E-04 1.9111633E-02 at 180iterations finished qdiffx linear iterations at : 23:52:23 total time elapsed so far: 12.58000 # loops : 180 mean,max change (kT/e) : 7.3578104E-04 1.9111633E-02 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 23:52:23 12.710u 0.244s 0:13.33 97.1% 0+0k 0+0io 0pf+0w