Mon Oct 10 14:04:31 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 Mon Oct 10 2011 at 14:04:31 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5176 !!! WARNING: HIZ 652 has a net charge of 0.2000 !!! WARNING: ZN7 714 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5181951 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): 24.42400 85.03400 ymin,ymax (A): 15.12900 82.45600 zmin,zma (A): -35.09500 33.60500 x,y,z range (A): 60.61000 67.32700 68.70000 scale (grids/A): 0.5181951 object centre (A): 54.72900 48.79250 -0.7449989 number of atom coordinates read : 5176 total number of charged atoms : 5006 net assigned charge : -1.399960 assigned positive charge : 792.9569 centred at (gu) : 90.72148 89.81628 90.60199 assigned negative charge : -794.3633 centred at (gu) : 90.65096 89.86240 90.64244 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8479 nv = 96 ne = 84 npr = 106908 no. pairs analyzed = 106908 no. exposed pairs = 5936 no. arc points = 40536 no. surface atoms = 2018 nbur = 3158 mkacc time = 0.2200000 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 = 1.652000 m= 300 mr = 4683 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.4600000 number of dielectric boundary points 4081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3984 ## 588 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 11503 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1131795E-10 -2.2359745E-10 midg,1,midg; midg,igrid,midg 1.6051807E-10 -2.0351593E-10 1,midg,midg; igrid,midg,midg -2.5830532E-10 3.0102237E-10 gauss-seidel spectral radius is 0.9809670 estimated iterations to convergence 60 setup time was (sec) 0.6700000 now iterating at: 14:04:31 rms-change max change #iterations 7.8036472E-02 10.84944 at 10iterations 7.1004955E-03 1.205223 at 20iterations 1.8306996E-03 0.3360634 at 30iterations 5.9962575E-04 0.1118584 at 40iterations 1.9739433E-04 3.7090302E-02 at 50iterations finished qdiffx linear iterations at : 14:04:34 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 1.9739433E-04 3.7090302E-02 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 14:04:35 3.256u 0.147s 0:04.06 83.4% 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 Mon Oct 10 2011 at 14:04:35 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5176 !!! WARNING: HIZ 652 has a net charge of 0.2000 !!! WARNING: ZN7 714 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.554585 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): 24.42400 85.03400 ymin,ymax (A): 15.12900 82.45600 zmin,zma (A): -35.09500 33.60500 x,y,z range (A): 60.61000 67.32700 68.70000 scale (grids/A): 1.554585 object centre (A): 54.72900 48.79250 -0.7449989 number of atom coordinates read : 5176 total number of charged atoms : 5006 net assigned charge : -1.399960 assigned positive charge : 792.9569 centred at (gu) : 92.16293 89.44765 91.80421 assigned negative charge : -794.3633 centred at (gu) : 91.95266 89.58670 91.92682 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 96460 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40536 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 28734 mr = 68308 m= 2616 mr = 20137 m= 60 mr = 1306 m= 0 mr = 4 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1935 time to turn everything in is 0.6700000 number of dielectric boundary points 38115 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 515 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 37759 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) : 0.5181951 object centre at (A) : 54.72900 48.79250 -0.7449989 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1802057E-02 3.8702038E-04 midg,1,midg; midg,igrid,midg 2.2305112E-02 -1.7744465E-02 1,midg,midg; igrid,midg,midg -7.1663936E-03 1.5828146E-02 gauss-seidel spectral radius is 0.9981912 estimated iterations to convergence 187 setup time was (sec) 0.9500000 now iterating at: 14:04:36 rms-change max change #iterations 4.151073 154.2223 at 10iterations 1.737558 56.29609 at 20iterations 0.7295980 24.20700 at 30iterations 0.3066569 10.04952 at 40iterations 0.1283002 4.351456 at 50iterations 5.4294668E-02 1.573978 at 60iterations 2.3091039E-02 0.7368641 at 70iterations 1.0095617E-02 0.3196259 at 80iterations 4.6322579E-03 0.1548233 at 90iterations 2.3142956E-03 8.2481384E-02 at 100iterations 1.2712581E-03 4.8133850E-02 at 110iterations 7.5983832E-04 2.7107239E-02 at 120iterations finished qdiffx linear iterations at : 14:04:42 total time elapsed so far: 6.910000 # loops : 120 mean,max change (kT/e) : 7.5983832E-04 2.7107239E-02 energy calculations done at 6.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.090000 DelPhi exited at 14:04:43 7.097u 0.160s 0:07.80 92.9% 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 Mon Oct 10 2011 at 14:04:43 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5176 !!! WARNING: HIZ 652 has a net charge of 0.2000 !!! WARNING: ZN7 714 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.331878 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): 24.42400 85.03400 ymin,ymax (A): 15.12900 82.45600 zmin,zma (A): -35.09500 33.60500 x,y,z range (A): 60.61000 67.32700 68.70000 scale (grids/A): 2.331878 object centre (A): 54.72900 48.79250 -0.7449989 number of atom coordinates read : 5176 total number of charged atoms : 5006 net assigned charge : -1.399960 assigned positive charge : 792.9569 centred at (gu) : 93.24404 89.17108 92.70593 assigned negative charge : -794.3633 centred at (gu) : 92.92883 89.38012 92.89062 start vw surface at 0.2100000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 225026 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40536 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 102070 mr = 167271 m= 27057 mr = 81792 m= 3894 mr = 20507 m= 233 mr = 2540 m= 6 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 6816 time to turn everything in is 1.530000 number of dielectric boundary points 86082 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 51 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 39955 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) : 1.554585 object centre at (A) : 54.72900 48.79250 -0.7449989 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2320680 0.1059374 midg,1,midg; midg,igrid,midg 0.4229249 -0.3936111 1,midg,midg; igrid,midg,midg -8.6560667E-02 0.4292406 gauss-seidel spectral radius is 0.9991840 estimated iterations to convergence 276 setup time was (sec) 1.820000 now iterating at: 14:04:45 rms-change max change #iterations 11.00273 294.8226 at 10iterations 6.329255 132.3689 at 20iterations 3.600438 78.53254 at 30iterations 2.042768 42.67870 at 40iterations 1.155026 21.77665 at 50iterations 0.6498784 12.63776 at 60iterations 0.3664301 6.471951 at 70iterations 0.2063614 3.651138 at 80iterations 0.1157001 2.113930 at 90iterations 6.4864725E-02 1.137903 at 100iterations 3.6401380E-02 0.7831421 at 110iterations 2.0379191E-02 0.3584518 at 120iterations 1.1465641E-02 0.1934052 at 130iterations 6.4851390E-03 0.1133270 at 140iterations 3.6799519E-03 7.1418762E-02 at 150iterations 2.1102102E-03 3.8482666E-02 at 160iterations 1.2348029E-03 2.3521423E-02 at 170iterations 7.4534421E-04 1.4705658E-02 at 180iterations finished qdiffx linear iterations at : 14:04:54 total time elapsed so far: 11.27000 # loops : 180 mean,max change (kT/e) : 7.4534421E-04 1.4705658E-02 energy calculations done at 11.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.43000 DelPhi exited at 14:04:55 11.435u 0.187s 0:12.30 94.3% 0+0k 0+0io 0pf+0w