Sat Oct 15 11:27:44 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 Sat Oct 15 2011 at 11:27:45 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 = 4525 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: 0.5763502 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): -6.275000 51.99100 ymin,ymax (A): 95.52700 157.2950 zmin,zma (A): -10.42900 48.10100 x,y,z range (A): 58.26600 61.76800 58.53000 scale (grids/A): 0.5763502 object centre (A): 22.85800 126.4110 18.83600 number of atom coordinates read : 4525 total number of charged atoms : 4355 net assigned charge : 5.000041 assigned positive charge : 691.9131 centred at (gu) : 89.40586 90.41740 90.56719 assigned negative charge : -686.9174 centred at (gu) : 89.40162 90.47466 90.53306 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 9708 nv = 96 ne = 84 npr = 92021 no. pairs analyzed = 92021 no. exposed pairs = 5532 no. arc points = 38094 no. surface atoms = 1858 nbur = 2667 mkacc time = 0.1600000 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 = 1.484000 m= 468 mr = 5290 m= 0 mr = 33 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4853 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3899 ## 434 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 12656 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4288719E-11 2.2706210E-09 midg,1,midg; midg,igrid,midg 2.4261197E-09 -8.5961599E-10 1,midg,midg; igrid,midg,midg 9.5645003E-10 9.5260466E-10 gauss-seidel spectral radius is 0.9845812 estimated iterations to convergence 66 setup time was (sec) 0.6000000 now iterating at: 11:27:46 rms-change max change #iterations 0.1201270 17.15713 at 10iterations 1.0553379E-02 1.306053 at 20iterations 2.5830788E-03 0.4018288 at 30iterations 1.3043062E-03 0.2121696 at 40iterations 6.9096475E-04 0.1128044 at 50iterations finished qdiffx linear iterations at : 11:27:49 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 6.9096475E-04 0.1128044 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 11:27:50 4.197u 0.299s 0:05.38 83.2% 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 Sat Oct 15 2011 at 11:27:50 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 = 4525 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.729051 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): -6.275000 51.99100 ymin,ymax (A): 95.52700 157.2950 zmin,zma (A): -10.42900 48.10100 x,y,z range (A): 58.26600 61.76800 58.53000 scale (grids/A): 1.729051 object centre (A): 22.85800 126.4110 18.83600 number of atom coordinates read : 4525 total number of charged atoms : 4355 net assigned charge : 5.000041 assigned positive charge : 691.9131 centred at (gu) : 88.21616 91.25040 91.70058 assigned negative charge : -686.9174 centred at (gu) : 88.20430 91.42374 91.59869 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 107938 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38094 grid for indexing accessible points = 1.400000 m= 36301 mr = 75987 m= 4803 mr = 25511 m= 219 mr = 2602 m= 3 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 538 time to turn everything in is 0.5300000 number of dielectric boundary points 45119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 399 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 33770 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) : 0.5763502 object centre at (A) : 22.85800 126.4110 18.83600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5334368E-03 3.9449543E-02 midg,1,midg; midg,igrid,midg 3.5014864E-02 -3.6563575E-02 1,midg,midg; igrid,midg,midg -1.8717736E-07 3.3555035E-02 gauss-seidel spectral radius is 0.9985376 estimated iterations to convergence 207 setup time was (sec) 0.7800000 now iterating at: 11:27:51 rms-change max change #iterations 4.858994 165.3507 at 10iterations 2.206226 66.54581 at 20iterations 1.004651 28.80755 at 30iterations 0.4580096 12.48615 at 40iterations 0.2093118 6.381809 at 50iterations 9.5890358E-02 2.826585 at 60iterations 4.4130586E-02 1.215341 at 70iterations 2.0571267E-02 0.5221291 at 80iterations 9.8916888E-03 0.2765808 at 90iterations 5.1714224E-03 0.1669979 at 100iterations 3.0905332E-03 0.1009369 at 110iterations 2.1100477E-03 6.9868088E-02 at 120iterations finished qdiffx linear iterations at : 11:28:01 total time elapsed so far: 10.11000 # loops : 120 mean,max change (kT/e) : 2.1100477E-03 6.9868088E-02 energy calculations done at 10.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.24000 DelPhi exited at 11:28:02 10.245u 0.299s 0:11.43 92.1% 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 Sat Oct 15 2011 at 11:28:02 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 = 4525 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: 2.593576 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): -6.275000 51.99100 ymin,ymax (A): 95.52700 157.2950 zmin,zma (A): -10.42900 48.10100 x,y,z range (A): 58.26600 61.76800 58.53000 scale (grids/A): 2.593576 object centre (A): 22.85800 126.4110 18.83600 number of atom coordinates read : 4525 total number of charged atoms : 4355 net assigned charge : 5.000041 assigned positive charge : 691.9131 centred at (gu) : 87.32376 91.87537 92.55050 assigned negative charge : -686.9174 centred at (gu) : 87.30625 92.13531 92.39788 start vw surface at 0.1200000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 250474 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38094 grid for indexing accessible points = 1.400000 m= 122673 mr = 185272 m= 38630 mr = 98381 m= 7944 mr = 29238 m= 906 mr = 5525 m= 22 mr = 493 m= 0 mr = 2 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 1758 time to turn everything in is 1.520000 number of dielectric boundary points 101738 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 34817 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) : 1.729051 object centre at (A) : 22.85800 126.4110 18.83600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2020106 0.5042614 midg,1,midg; midg,igrid,midg 0.7531860 -0.6716715 1,midg,midg; igrid,midg,midg -4.1895024E-02 0.6265736 gauss-seidel spectral radius is 0.9992737 estimated iterations to convergence 293 setup time was (sec) 1.910000 now iterating at: 11:28:04 rms-change max change #iterations 11.95879 320.6135 at 10iterations 7.075657 151.0146 at 20iterations 4.159122 80.11829 at 30iterations 2.440138 43.72683 at 40iterations 1.426753 27.15244 at 50iterations 0.8321055 13.78529 at 60iterations 0.4834329 7.565033 at 70iterations 0.2818102 5.318897 at 80iterations 0.1636215 2.782377 at 90iterations 9.5168687E-02 1.623819 at 100iterations 5.5251390E-02 0.8825207 at 110iterations 3.2244977E-02 0.5093937 at 120iterations 1.8988756E-02 0.3474331 at 130iterations 1.1306739E-02 0.2169437 at 140iterations 6.9785560E-03 0.1304722 at 150iterations 4.5479978E-03 9.0667725E-02 at 160iterations 3.1890161E-03 6.5423489E-02 at 170iterations 2.4179034E-03 4.8969269E-02 at 180iterations finished qdiffx linear iterations at : 11:28:23 total time elapsed so far: 17.38000 # loops : 180 mean,max change (kT/e) : 2.4179034E-03 4.8969269E-02 energy calculations done at 17.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.50000 DelPhi exited at 11:28:24 17.506u 0.414s 0:22.47 79.7% 0+0k 0+0io 0pf+0w