Tue Oct 11 07:13:19 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 Tue Oct 11 2011 at 07:13:19 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 = 2542 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: 0.6618207 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): -54.51600 -0.7250000 ymin,ymax (A): -28.42800 24.11500 zmin,zma (A): -1.763000 44.03900 x,y,z range (A): 53.79100 52.54300 45.80200 scale (grids/A): 0.6618207 object centre (A): -27.62050 -2.156500 21.13800 number of atom coordinates read : 2542 total number of charged atoms : 2403 net assigned charge : -3.499995 assigned positive charge : 375.7351 centred at (gu) : 90.05721 90.93394 88.54158 assigned negative charge : -379.2356 centred at (gu) : 89.92120 90.88870 88.40029 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7698 nv = 96 ne = 84 npr = 51490 no. pairs analyzed = 51490 no. exposed pairs = 3222 no. arc points = 22291 no. surface atoms = 1100 nbur = 1442 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 425 mr = 4351 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2069 ## 163 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8813 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1525408E-08 1.4009257E-08 midg,1,midg; midg,igrid,midg -1.4948688E-08 3.3343744E-10 1,midg,midg; igrid,midg,midg -3.6341465E-08 1.8374934E-08 gauss-seidel spectral radius is 0.9881659 estimated iterations to convergence 75 setup time was (sec) 0.6900000 now iterating at: 07:13:20 rms-change max change #iterations 0.1662629 24.77592 at 10iterations 1.8290183E-02 2.668945 at 20iterations 1.9897709E-03 0.2950296 at 30iterations 2.6390763E-04 4.8925400E-02 at 40iterations 5.5233311E-05 1.0253906E-02 at 50iterations finished qdiffx linear iterations at : 07:13:23 total time elapsed so far: 3.970000 # loops : 50 mean,max change (kT/e) : 5.5233311E-05 1.0253906E-02 energy calculations done at 3.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.220000 DelPhi exited at 07:13:24 4.219u 0.172s 0:04.69 93.3% 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 Tue Oct 11 2011 at 07:13:24 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 = 2542 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: 1.985462 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): -54.51600 -0.7250000 ymin,ymax (A): -28.42800 24.11500 zmin,zma (A): -1.763000 44.03900 x,y,z range (A): 53.79100 52.54300 45.80200 scale (grids/A): 1.985462 object centre (A): -27.62050 -2.156500 21.13800 number of atom coordinates read : 2542 total number of charged atoms : 2403 net assigned charge : -3.499995 assigned positive charge : 375.7351 centred at (gu) : 90.17125 92.80146 85.62448 assigned negative charge : -379.2356 centred at (gu) : 89.76338 92.66591 85.20076 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 82045 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22291 grid for indexing accessible points = 1.400000 m= 32042 mr = 57618 m= 5668 mr = 24441 m= 433 mr = 3810 m= 7 mr = 198 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 571 time to turn everything in is 0.7500000 number of dielectric boundary points 34128 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 18989 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) : 0.6618207 object centre at (A) : -27.62050 -2.156500 21.13800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9059354E-02 2.1046858E-02 midg,1,midg; midg,igrid,midg -3.5626922E-02 -4.1730609E-02 1,midg,midg; igrid,midg,midg -4.0874891E-02 -3.3934712E-02 gauss-seidel spectral radius is 0.9987381 estimated iterations to convergence 223 setup time was (sec) 1.120000 now iterating at: 07:13:25 rms-change max change #iterations 4.548204 190.7818 at 10iterations 2.204155 82.38372 at 20iterations 1.061861 37.38519 at 30iterations 0.5118948 15.41113 at 40iterations 0.2472573 6.763590 at 50iterations 0.1196293 3.526714 at 60iterations 5.7909355E-02 1.628415 at 70iterations 2.8011406E-02 0.8632011 at 80iterations 1.3503342E-02 0.4138050 at 90iterations 6.5351683E-03 0.1960430 at 100iterations 3.1720113E-03 9.9167824E-02 at 110iterations 1.5493627E-03 4.8191071E-02 at 120iterations finished qdiffx linear iterations at : 07:13:33 total time elapsed so far: 9.400000 # loops : 120 mean,max change (kT/e) : 1.5493627E-03 4.8191071E-02 energy calculations done at 9.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.630000 DelPhi exited at 07:13:34 9.634u 0.236s 0:10.22 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 Tue Oct 11 2011 at 07:13:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2542 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: 2.978193 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): -54.51600 -0.7250000 ymin,ymax (A): -28.42800 24.11500 zmin,zma (A): -1.763000 44.03900 x,y,z range (A): 53.79100 52.54300 45.80200 scale (grids/A): 2.978193 object centre (A): -27.62050 -2.156500 21.13800 number of atom coordinates read : 2542 total number of charged atoms : 2403 net assigned charge : -3.499995 assigned positive charge : 375.7351 centred at (gu) : 90.25669 94.20210 83.43655 assigned negative charge : -379.2356 centred at (gu) : 89.64504 93.99866 82.80115 start vw surface at 0.1800000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 189489 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22291 grid for indexing accessible points = 1.400000 m= 100652 mr = 138844 m= 39744 mr = 83876 m= 10450 mr = 32967 m= 1794 mr = 8185 m= 129 mr = 1314 m= 3 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 2007 time to turn everything in is 1.970000 number of dielectric boundary points 77017 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 19224 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) : 1.985462 object centre at (A) : -27.62050 -2.156500 21.13800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4733630 0.1528812 midg,1,midg; midg,igrid,midg -0.4751720 -0.5815912 1,midg,midg; igrid,midg,midg -0.2647291 -0.4075234 gauss-seidel spectral radius is 0.9992875 estimated iterations to convergence 296 setup time was (sec) 2.350000 now iterating at: 07:13:36 rms-change max change #iterations 10.44521 463.9616 at 10iterations 6.134377 143.3166 at 20iterations 3.594849 73.17801 at 30iterations 2.102150 36.47346 at 40iterations 1.223626 23.14892 at 50iterations 0.7133767 14.31275 at 60iterations 0.4162407 7.389891 at 70iterations 0.2416777 4.228525 at 80iterations 0.1403464 2.602180 at 90iterations 8.1716776E-02 1.382230 at 100iterations 4.7412809E-02 0.9055862 at 110iterations 2.7514854E-02 0.4964848 at 120iterations 1.5987542E-02 0.2751160 at 130iterations 9.2945946E-03 0.1568218 at 140iterations 5.4191658E-03 9.0824127E-02 at 150iterations 3.1587926E-03 5.6015968E-02 at 160iterations 1.8586004E-03 3.2851696E-02 at 170iterations 1.1017270E-03 1.7519951E-02 at 180iterations finished qdiffx linear iterations at : 07:13:52 total time elapsed so far: 17.53000 # loops : 180 mean,max change (kT/e) : 1.1017270E-03 1.7519951E-02 energy calculations done at 17.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.76000 DelPhi exited at 07:13:52 17.764u 0.263s 0:18.31 98.4% 0+0k 0+0io 0pf+0w