Sun Oct 9 13:07:11 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 13:07:11 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 = 2365 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6916248 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): -6.858000 44.61500 ymin,ymax (A): -14.09200 36.54400 zmin,zma (A): 2.076000 45.53700 x,y,z range (A): 51.47300 50.63600 43.46100 scale (grids/A): 0.6916248 object centre (A): 18.87850 11.22600 23.80650 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500012 assigned positive charge : 359.3971 centred at (gu) : 89.63803 91.40820 90.50338 assigned negative charge : -354.8976 centred at (gu) : 89.69138 91.53865 90.52349 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7754 nv = 96 ne = 84 npr = 46925 no. pairs analyzed = 46925 no. exposed pairs = 3003 no. arc points = 21287 no. surface atoms = 1015 nbur = 1350 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 485 mr = 4263 m= 1 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 7.9999991E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3900 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2002 ## 193 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8715 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1295141E-08 2.0642998E-08 midg,1,midg; midg,igrid,midg 5.8271379E-08 -3.4047979E-08 1,midg,midg; igrid,midg,midg 5.0931092E-08 5.3818421E-09 gauss-seidel spectral radius is 0.9891406 estimated iterations to convergence 78 setup time was (sec) 0.3800000 now iterating at: 13:07:11 rms-change max change #iterations 0.1921690 25.70330 at 10iterations 2.3016941E-02 3.473524 at 20iterations 3.1397985E-03 0.4790621 at 30iterations 6.6502910E-04 0.1188812 at 40iterations 2.1753875E-04 3.5322189E-02 at 50iterations finished qdiffx linear iterations at : 13:07:14 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 2.1753875E-04 3.5322189E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 13:07:14 3.410u 0.177s 0:03.86 92.7% 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 13:07:14 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 = 2365 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.074874 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): -6.858000 44.61500 ymin,ymax (A): -14.09200 36.54400 zmin,zma (A): 2.076000 45.53700 x,y,z range (A): 51.47300 50.63600 43.46100 scale (grids/A): 2.074874 object centre (A): 18.87850 11.22600 23.80650 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500012 assigned positive charge : 359.3971 centred at (gu) : 88.91382 94.22421 91.50954 assigned negative charge : -354.8976 centred at (gu) : 89.07395 94.61561 91.57030 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 82400 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21287 grid for indexing accessible points = 1.400000 m= 31487 mr = 57183 m= 5451 mr = 23177 m= 457 mr = 3331 m= 21 mr = 238 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 35887 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 17633 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) : 0.6916248 object centre at (A) : 18.87850 11.22600 23.80650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6988260E-02 1.3528307E-02 midg,1,midg; midg,igrid,midg 1.7776396E-02 -1.9531209E-02 1,midg,midg; igrid,midg,midg 5.2523833E-02 -2.8613918E-02 gauss-seidel spectral radius is 0.9988225 estimated iterations to convergence 231 setup time was (sec) 0.6400000 now iterating at: 13:07:15 rms-change max change #iterations 4.788222 219.5866 at 10iterations 2.348653 83.38299 at 20iterations 1.158637 36.78265 at 30iterations 0.5762421 16.44332 at 40iterations 0.2831855 8.384779 at 50iterations 0.1400778 4.247005 at 60iterations 6.9572628E-02 2.056611 at 70iterations 3.4509286E-02 1.046250 at 80iterations 1.7130475E-02 0.5641251 at 90iterations 8.6246757E-03 0.2754021 at 100iterations 4.4169487E-03 0.1260452 at 110iterations 2.3311931E-03 8.1652641E-02 at 120iterations finished qdiffx linear iterations at : 13:07:22 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 2.3311931E-03 8.1652641E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 13:07:23 7.980u 0.199s 0:08.44 96.8% 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 13:07:23 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 = 2365 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.112311 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): -6.858000 44.61500 ymin,ymax (A): -14.09200 36.54400 zmin,zma (A): 2.076000 45.53700 x,y,z range (A): 51.47300 50.63600 43.46100 scale (grids/A): 3.112311 object centre (A): 18.87850 11.22600 23.80650 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500012 assigned positive charge : 359.3971 centred at (gu) : 88.37062 96.33614 92.26428 assigned negative charge : -354.8976 centred at (gu) : 88.61079 96.92333 92.35526 start vw surface at 0.1000000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 189918 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21287 grid for indexing accessible points = 1.400000 m= 99567 mr = 137877 m= 38345 mr = 81574 m= 9963 mr = 30771 m= 1792 mr = 7334 m= 255 mr = 1213 m= 11 mr = 187 m= 0 mr = 2 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 80893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 17794 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) : 2.074874 object centre at (A) : 18.87850 11.22600 23.80650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4449125 3.9794497E-02 midg,1,midg; midg,igrid,midg 0.3430749 -0.1738583 1,midg,midg; igrid,midg,midg 0.6441826 -0.6435601 gauss-seidel spectral radius is 0.9992980 estimated iterations to convergence 298 setup time was (sec) 1.490000 now iterating at: 13:07:25 rms-change max change #iterations 10.76254 411.8941 at 10iterations 6.409694 136.4137 at 20iterations 3.800658 66.20560 at 30iterations 2.250071 41.23891 at 40iterations 1.331492 23.18681 at 50iterations 0.7841105 14.81268 at 60iterations 0.4612798 10.44697 at 70iterations 0.2705561 4.592472 at 80iterations 0.1591208 2.632755 at 90iterations 9.3346842E-02 1.564408 at 100iterations 5.4804061E-02 1.030113 at 110iterations 3.2287441E-02 0.5775070 at 120iterations 1.9139510E-02 0.3537598 at 130iterations 1.1494521E-02 0.2222824 at 140iterations 7.0641618E-03 0.1493683 at 150iterations 4.5172255E-03 0.1024628 at 160iterations 3.0602801E-03 6.3343048E-02 at 170iterations 2.2104315E-03 4.7458649E-02 at 180iterations finished qdiffx linear iterations at : 13:07:36 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 2.2104315E-03 4.7458649E-02 energy calculations done at 12.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 13:07:36 13.082u 0.196s 0:13.56 97.8% 0+0k 0+0io 0pf+0w