Sun Oct 9 22:42:08 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 Sun Oct 9 2011 at 22:42:08 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 = 3036 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: 0.6758808 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): -31.89400 20.44500 ymin,ymax (A): -2.263000 49.88800 zmin,zma (A): 15.15400 67.82600 x,y,z range (A): 52.33900 52.15100 52.67200 scale (grids/A): 0.6758808 object centre (A): -5.724501 23.81250 41.49000 number of atom coordinates read : 3036 total number of charged atoms : 2984 net assigned charge : 7.500010 assigned positive charge : 474.1698 centred at (gu) : 89.35923 90.98564 90.47418 assigned negative charge : -466.6711 centred at (gu) : 89.48628 91.11494 90.47632 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 9709 nv = 96 ne = 84 npr = 56689 no. pairs analyzed = 56689 no. exposed pairs = 4144 no. arc points = 29925 no. surface atoms = 1370 nbur = 1666 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 668 mr = 5123 m= 4 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 115 time to turn everything in is 0.3700000 number of dielectric boundary points 5148 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2793 ## 287 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 11379 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7315462E-08 3.1244731E-08 midg,1,midg; midg,igrid,midg 6.0899545E-08 -2.1455550E-08 1,midg,midg; igrid,midg,midg 8.3818520E-08 -1.4070774E-08 gauss-seidel spectral radius is 0.9887083 estimated iterations to convergence 77 setup time was (sec) 0.6000000 now iterating at: 22:42:09 rms-change max change #iterations 0.2024061 25.87378 at 10iterations 2.2410886E-02 2.791838 at 20iterations 2.5036579E-03 0.3139381 at 30iterations 2.8159557E-04 3.2497406E-02 at 40iterations 3.1811865E-05 4.0626526E-03 at 50iterations finished qdiffx linear iterations at : 22:42:11 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 3.1811865E-05 4.0626526E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 22:42:12 3.392u 0.153s 0:03.96 89.3% 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 Sun Oct 9 2011 at 22:42:12 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 = 3036 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: 2.027642 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): -31.89400 20.44500 ymin,ymax (A): -2.263000 49.88800 zmin,zma (A): 15.15400 67.82600 x,y,z range (A): 52.33900 52.15100 52.67200 scale (grids/A): 2.027642 object centre (A): -5.724501 23.81250 41.49000 number of atom coordinates read : 3036 total number of charged atoms : 2984 net assigned charge : 7.500010 assigned positive charge : 474.1698 centred at (gu) : 88.07645 92.95588 91.42184 assigned negative charge : -466.6711 centred at (gu) : 88.45863 93.34431 91.42844 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 103389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29925 grid for indexing accessible points = 1.400000 m= 39931 mr = 69723 m= 7833 mr = 29014 m= 730 mr = 5037 m= 22 mr = 370 m= 0 mr = 2 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 2685 time to turn everything in is 0.7500000 number of dielectric boundary points 47759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 142 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 23591 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) : 0.6758808 object centre at (A) : -5.724501 23.81250 41.49000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1805141E-03 1.0894809E-02 midg,1,midg; midg,igrid,midg 5.5929694E-02 6.4044252E-02 1,midg,midg; igrid,midg,midg 3.3675555E-02 9.7666765E-03 gauss-seidel spectral radius is 0.9988515 estimated iterations to convergence 234 setup time was (sec) 1.040000 now iterating at: 22:42:13 rms-change max change #iterations 5.315694 241.0737 at 10iterations 2.641340 77.23911 at 20iterations 1.308010 38.53221 at 30iterations 0.6519507 17.96504 at 40iterations 0.3246703 8.374393 at 50iterations 0.1612336 4.330566 at 60iterations 8.0106743E-02 2.240223 at 70iterations 4.0009789E-02 1.088150 at 80iterations 1.9876279E-02 0.6019888 at 90iterations 9.8859509E-03 0.2556884 at 100iterations 4.9300571E-03 0.1306686 at 110iterations 2.4576397E-03 6.7840576E-02 at 120iterations finished qdiffx linear iterations at : 22:42:20 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 2.4576397E-03 6.7840576E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 22:42:20 7.791u 0.168s 0:08.34 95.3% 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 Sun Oct 9 2011 at 22:42:20 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 = 3036 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: 3.041464 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): -31.89400 20.44500 ymin,ymax (A): -2.263000 49.88800 zmin,zma (A): 15.15400 67.82600 x,y,z range (A): 52.33900 52.15100 52.67200 scale (grids/A): 3.041464 object centre (A): -5.724501 23.81250 41.49000 number of atom coordinates read : 3036 total number of charged atoms : 2984 net assigned charge : 7.500010 assigned positive charge : 474.1698 centred at (gu) : 87.11453 94.43367 92.13256 assigned negative charge : -466.6711 centred at (gu) : 87.68787 95.01645 92.14233 start vw surface at 0.1600000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 238033 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29925 grid for indexing accessible points = 1.400000 m= 124050 mr = 168854 m= 49891 mr = 100098 m= 14719 mr = 39799 m= 2968 mr = 11117 m= 319 mr = 2138 m= 5 mr = 194 m= 0 mr = 0 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 8916 time to turn everything in is 1.950000 number of dielectric boundary points 107785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 23872 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) : 2.027642 object centre at (A) : -5.724501 23.81250 41.49000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7822657E-02 -3.7889894E-02 midg,1,midg; midg,igrid,midg 0.3609076 0.6121529 1,midg,midg; igrid,midg,midg 0.4976849 0.2957162 gauss-seidel spectral radius is 0.9993497 estimated iterations to convergence 309 setup time was (sec) 2.270000 now iterating at: 22:42:23 rms-change max change #iterations 12.32607 347.2677 at 10iterations 7.547491 154.0332 at 20iterations 4.584380 87.47069 at 30iterations 2.786502 52.70451 at 40iterations 1.683896 34.30645 at 50iterations 1.015272 18.93349 at 60iterations 0.6119768 12.06683 at 70iterations 0.3670419 6.165189 at 80iterations 0.2202108 4.054036 at 90iterations 0.1318341 2.295232 at 100iterations 7.8984015E-02 1.324573 at 110iterations 4.7187734E-02 0.7188044 at 120iterations 2.8169530E-02 0.4652405 at 130iterations 1.6852442E-02 0.2810154 at 140iterations 1.0071596E-02 0.1521869 at 150iterations 6.0044774E-03 9.2836380E-02 at 160iterations 3.5849698E-03 5.8355331E-02 at 170iterations 2.1352349E-03 3.2661915E-02 at 180iterations finished qdiffx linear iterations at : 22:42:33 total time elapsed so far: 12.74000 # loops : 180 mean,max change (kT/e) : 2.1352349E-03 3.2661915E-02 energy calculations done at 12.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 22:42:34 12.940u 0.177s 0:13.55 96.7% 0+0k 0+0io 0pf+0w