Sat Oct 8 17:46:30 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 Sat Oct 8 2011 at 17:46:30 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 = 3482 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: 0.5040494 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): -11.99200 43.75000 ymin,ymax (A): -38.50500 32.12300 zmin,zma (A): -16.17500 34.79200 x,y,z range (A): 55.74200 70.62801 50.96700 scale (grids/A): 0.5040494 object centre (A): 15.87900 -3.191000 9.308500 number of atom coordinates read : 3482 total number of charged atoms : 3336 net assigned charge : -0.9999919 assigned positive charge : 524.6682 centred at (gu) : 89.77679 90.64613 90.42614 assigned negative charge : -525.6698 centred at (gu) : 89.82126 90.59744 90.36136 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5621 nv = 96 ne = 84 npr = 69649 no. pairs analyzed = 69649 no. exposed pairs = 4311 no. arc points = 30016 no. surface atoms = 1451 nbur = 2031 mkacc time = 0.1500000 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 = 1.680000 m= 188 mr = 2929 m= 0 mr = 10 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 2870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2968 ## 490 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7538 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.4180018E-11 9.0711931E-11 midg,1,midg; midg,igrid,midg -6.9046650E-11 6.9183964E-11 1,midg,midg; igrid,midg,midg 5.5223392E-11 -7.1538157E-11 gauss-seidel spectral radius is 0.9797823 estimated iterations to convergence 58 setup time was (sec) 0.5900000 now iterating at: 17:46:31 rms-change max change #iterations 5.2863501E-02 11.63142 at 10iterations 2.8868401E-03 0.5129700 at 20iterations 2.0020900E-04 3.3571005E-02 at 30iterations 2.6779819E-05 6.6242218E-03 at 40iterations 5.5685005E-06 1.5983582E-03 at 50iterations finished qdiffx linear iterations at : 17:46:34 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 5.5685005E-06 1.5983582E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 17:46:34 3.380u 0.204s 0:03.93 91.0% 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 Sat Oct 8 2011 at 17:46:34 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 = 3482 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: 1.512148 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): -11.99200 43.75000 ymin,ymax (A): -38.50500 32.12300 zmin,zma (A): -16.17500 34.79200 x,y,z range (A): 55.74200 70.62801 50.96700 scale (grids/A): 1.512148 object centre (A): 15.87900 -3.191000 9.308500 number of atom coordinates read : 3482 total number of charged atoms : 3336 net assigned charge : -0.9999919 assigned positive charge : 524.6682 centred at (gu) : 89.32943 91.93721 91.27722 assigned negative charge : -525.6698 centred at (gu) : 89.46352 91.79195 91.08396 start vw surface at 0.1800000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 64149 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30016 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 18770 mr = 44193 m= 1530 mr = 12731 m= 24 mr = 646 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 187 time to turn everything in is 0.4900000 number of dielectric boundary points 26903 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 450 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 24933 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) : 0.5040494 object centre at (A) : 15.87900 -3.191000 9.308500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0967307E-03 2.9815871E-03 midg,1,midg; midg,igrid,midg 5.3455601E-03 2.4934765E-03 1,midg,midg; igrid,midg,midg 2.6686655E-03 -4.9727829E-03 gauss-seidel spectral radius is 0.9979193 estimated iterations to convergence 174 setup time was (sec) 0.7800000 now iterating at: 17:46:35 rms-change max change #iterations 3.051005 149.1844 at 10iterations 1.196950 58.70976 at 20iterations 0.4709255 20.43789 at 30iterations 0.1845921 7.235947 at 40iterations 7.2546951E-02 2.665359 at 50iterations 2.8357562E-02 1.189795 at 60iterations 1.1196062E-02 0.4515152 at 70iterations 4.4037122E-03 0.1995773 at 80iterations 1.7353744E-03 6.9039583E-02 at 90iterations 6.8959559E-04 2.8141141E-02 at 100iterations 2.7767039E-04 9.8865628E-03 at 110iterations 1.1392275E-04 4.6494007E-03 at 120iterations finished qdiffx linear iterations at : 17:46:42 total time elapsed so far: 7.230000 # loops : 120 mean,max change (kT/e) : 1.1392275E-04 4.6494007E-03 energy calculations done at 7.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.400000 DelPhi exited at 17:46:42 7.407u 0.200s 0:07.88 96.4% 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 Sat Oct 8 2011 at 17:46:42 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3482 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: 2.268222 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): -11.99200 43.75000 ymin,ymax (A): -38.50500 32.12300 zmin,zma (A): -16.17500 34.79200 x,y,z range (A): 55.74200 70.62801 50.96700 scale (grids/A): 2.268222 object centre (A): 15.87900 -3.191000 9.308500 number of atom coordinates read : 3482 total number of charged atoms : 3336 net assigned charge : -0.9999919 assigned positive charge : 524.6682 centred at (gu) : 88.99402 92.90562 91.91560 assigned negative charge : -525.6698 centred at (gu) : 89.19514 92.68770 91.62584 start vw surface at 0.1900000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 149258 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30016 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 67569 mr = 108235 m= 17026 mr = 53458 m= 2190 mr = 12440 m= 87 mr = 1255 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 587 time to turn everything in is 1.130000 number of dielectric boundary points 60727 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 26596 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) : 1.512148 object centre at (A) : 15.87900 -3.191000 9.308500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9125500E-02 5.1617667E-02 midg,1,midg; midg,igrid,midg 0.1594710 3.8429480E-02 1,midg,midg; igrid,midg,midg 5.5381630E-02 -7.5527593E-02 gauss-seidel spectral radius is 0.9990608 estimated iterations to convergence 258 setup time was (sec) 1.440000 now iterating at: 17:46:44 rms-change max change #iterations 8.258073 288.1790 at 10iterations 4.501665 123.2771 at 20iterations 2.442742 58.60693 at 30iterations 1.321535 28.98446 at 40iterations 0.7118486 15.73818 at 50iterations 0.3830043 8.608782 at 60iterations 0.2060728 4.832364 at 70iterations 0.1105046 2.437137 at 80iterations 5.9413221E-02 1.304716 at 90iterations 3.1871170E-02 0.7927799 at 100iterations 1.7077480E-02 0.3811722 at 110iterations 9.1672465E-03 0.1951218 at 120iterations 4.8938086E-03 0.1159782 at 130iterations 2.6248605E-03 5.6583405E-02 at 140iterations 1.4098710E-03 3.1120300E-02 at 150iterations 7.5672730E-04 1.6700745E-02 at 160iterations 4.0789897E-04 9.0837479E-03 at 170iterations 2.1968166E-04 5.5856705E-03 at 180iterations finished qdiffx linear iterations at : 17:46:54 total time elapsed so far: 11.68000 # loops : 180 mean,max change (kT/e) : 2.1968166E-04 5.5856705E-03 energy calculations done at 11.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.85000 DelPhi exited at 17:46:55 11.852u 0.216s 0:12.34 97.7% 0+0k 0+0io 0pf+0w