Thu Jan 19 13:33:00 PST 2012 #!/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 Thu Jan 19 2012 at 13:33:01 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: 363 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6928 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4313008 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): -5.503000 77.03800 ymin,ymax (A): -1.053000 75.41900 zmin,zma (A): 159.2140 228.3830 x,y,z range (A): 82.54100 76.47200 69.16901 scale (grids/A): 0.4313008 object centre (A): 35.76750 37.18300 193.7985 number of atom coordinates read : 6928 total number of charged atoms : 6757 net assigned charge : 0.2000304 assigned positive charge : 1053.303 centred at (gu) : 88.99252 89.99548 89.52004 assigned negative charge : -1053.111 centred at (gu) : 89.00451 90.03474 89.49434 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7586 nv = 96 ne = 84 npr = 139601 no. pairs analyzed = 139601 no. exposed pairs = 9038 no. arc points = 61749 no. surface atoms = 3024 nbur = 3904 mkacc time = 0.2400000 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 = 1.932000 m= 193 mr = 3543 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5101 ## 1033 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 10528 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0252595E-12 1.5617283E-12 midg,1,midg; midg,igrid,midg 2.7459905E-12 -2.6859313E-12 1,midg,midg; igrid,midg,midg 1.1948090E-12 -5.7597883E-13 gauss-seidel spectral radius is 0.9727288 estimated iterations to convergence 51 setup time was (sec) 0.6500000 now iterating at: 13:33:02 rms-change max change #iterations 3.0668873E-02 5.737882 at 10iterations 2.0183080E-03 0.3411636 at 20iterations 5.8480923E-04 7.3837280E-02 at 30iterations 1.9829441E-04 2.7750492E-02 at 40iterations 6.7819994E-05 1.0581970E-02 at 50iterations finished qdiffx linear iterations at : 13:33:06 total time elapsed so far: 3.800000 # loops : 50 mean,max change (kT/e) : 6.7819994E-05 1.0581970E-02 energy calculations done at 3.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.950000 DelPhi exited at 13:33:06 3.957u 0.184s 0:05.32 77.6% 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 Thu Jan 19 2012 at 13:33:06 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: 363 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6928 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.293902 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): -5.503000 77.03800 ymin,ymax (A): -1.053000 75.41900 zmin,zma (A): 159.2140 228.3830 x,y,z range (A): 82.54100 76.47200 69.16901 scale (grids/A): 1.293902 object centre (A): 35.76750 37.18300 193.7985 number of atom coordinates read : 6928 total number of charged atoms : 6757 net assigned charge : 0.2000304 assigned positive charge : 1053.303 centred at (gu) : 86.97521 89.98449 88.55824 assigned negative charge : -1053.111 centred at (gu) : 87.01331 90.10391 88.48282 start vw surface at 0.1900000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 88680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 61749 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 20512 mr = 58306 m= 1034 mr = 11902 m= 6 mr = 228 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 478 time to turn everything in is 0.5000000 number of dielectric boundary points 39796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1106 ## 43 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 46956 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) : 0.4313008 object centre at (A) : 35.76750 37.18300 193.7985 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3707066E-04 -4.3512071E-05 midg,1,midg; midg,igrid,midg -8.1911474E-04 -4.4239997E-03 1,midg,midg; igrid,midg,midg 1.4078610E-03 3.5257135E-03 gauss-seidel spectral radius is 0.9974365 estimated iterations to convergence 157 setup time was (sec) 0.7300000 now iterating at: 13:33:07 rms-change max change #iterations 3.095812 129.4512 at 10iterations 1.096482 36.37294 at 20iterations 0.3863968 14.91922 at 30iterations 0.1373808 4.505787 at 40iterations 4.8914075E-02 1.721809 at 50iterations 1.7441604E-02 0.6654606 at 60iterations 6.3305269E-03 0.2135372 at 70iterations 2.4458913E-03 8.1231117E-02 at 80iterations 1.0801059E-03 3.6125183E-02 at 90iterations 5.7412189E-04 1.8384933E-02 at 100iterations 3.5214701E-04 1.0269165E-02 at 110iterations 2.2921519E-04 6.2866211E-03 at 120iterations finished qdiffx linear iterations at : 13:33:21 total time elapsed so far: 8.090000 # loops : 120 mean,max change (kT/e) : 2.2921519E-04 6.2866211E-03 energy calculations done at 8.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.220000 DelPhi exited at 13:33:22 8.219u 0.219s 0:15.89 52.9% 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 Thu Jan 19 2012 at 13:33:22 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: 363 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6928 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.940854 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): -5.503000 77.03800 ymin,ymax (A): -1.053000 75.41900 zmin,zma (A): 159.2140 228.3830 x,y,z range (A): 82.54100 76.47200 69.16901 scale (grids/A): 1.940854 object centre (A): 35.76750 37.18300 193.7985 number of atom coordinates read : 6928 total number of charged atoms : 6757 net assigned charge : 0.2000304 assigned positive charge : 1053.303 centred at (gu) : 85.46235 89.97636 87.83669 assigned negative charge : -1053.111 centred at (gu) : 85.51981 90.15562 87.72407 start vw surface at 0.1700000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 208381 reading accessible surface arcs data from file ARCDAT no. of arc points read = 61749 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 79776 mr = 145915 m= 14198 mr = 58461 m= 1037 mr = 8817 m= 12 mr = 389 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 1551 time to turn everything in is 1.090000 number of dielectric boundary points 89822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 331 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 53327 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) : 1.293902 object centre at (A) : 35.76750 37.18300 193.7985 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.9542015E-04 -7.9964902E-03 midg,1,midg; midg,igrid,midg -3.7750740E-02 -7.7613108E-02 1,midg,midg; igrid,midg,midg 0.1457553 0.1576448 gauss-seidel spectral radius is 0.9989926 estimated iterations to convergence 249 setup time was (sec) 1.370000 now iterating at: 13:33:24 rms-change max change #iterations 9.553271 249.8668 at 10iterations 5.186697 135.0014 at 20iterations 2.789537 71.06862 at 30iterations 1.490453 33.92051 at 40iterations 0.7927878 18.14540 at 50iterations 0.4207319 9.711819 at 60iterations 0.2229684 5.067271 at 70iterations 0.1175128 2.385544 at 80iterations 6.1997060E-02 1.387934 at 90iterations 3.2657530E-02 0.8458855 at 100iterations 1.7207503E-02 0.3380604 at 110iterations 9.0297889E-03 0.2006836 at 120iterations 4.7530700E-03 0.1030121 at 130iterations 2.4920928E-03 5.3794861E-02 at 140iterations 1.3087970E-03 2.7410507E-02 at 150iterations 6.8874535E-04 1.3028979E-02 at 160iterations 3.6196870E-04 7.3585510E-03 at 170iterations 1.9097330E-04 3.7508011E-03 at 180iterations finished qdiffx linear iterations at : 13:33:36 total time elapsed so far: 13.54000 # loops : 180 mean,max change (kT/e) : 1.9097330E-04 3.7508011E-03 energy calculations done at 13.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.67000 DelPhi exited at 13:33:37 13.667u 0.247s 0:14.75 94.2% 0+0k 0+0io 0pf+0w