Sun Oct 9 08:16:22 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 Sun Oct 9 2011 at 08:16:22 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5601 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: 0.5393940 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): -16.78500 49.21500 ymin,ymax (A): 4.250000 68.83100 zmin,zma (A): -110.3780 -45.84200 x,y,z range (A): 66.00000 64.58100 64.53600 scale (grids/A): 0.5393940 object centre (A): 16.21500 36.54050 -78.11000 number of atom coordinates read : 5601 total number of charged atoms : 5435 net assigned charge : -2.499965 assigned positive charge : 841.4996 centred at (gu) : 90.20056 91.15836 89.25073 assigned negative charge : -844.0068 centred at (gu) : 90.18250 91.13279 89.12326 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 10403 nv = 96 ne = 84 npr = 113096 no. pairs analyzed = 113096 no. exposed pairs = 7165 no. arc points = 49444 no. surface atoms = 2413 nbur = 3188 mkacc time = 0.1900000 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 = 1.596000 m= 418 mr = 5436 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 58 time to turn everything in is 0.3700000 number of dielectric boundary points 5370 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4957 ## 663 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 13910 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6750868E-09 9.2443464E-10 midg,1,midg; midg,igrid,midg -2.7278840E-10 1.8781283E-10 1,midg,midg; igrid,midg,midg -2.7573643E-10 6.8270466E-11 gauss-seidel spectral radius is 0.9824809 estimated iterations to convergence 62 setup time was (sec) 0.5600000 now iterating at: 08:16:23 rms-change max change #iterations 9.8936826E-02 12.83874 at 10iterations 6.5446268E-03 0.7690463 at 20iterations 6.0978619E-04 0.1139488 at 30iterations 1.3521526E-04 3.0084610E-02 at 40iterations 4.1861629E-05 9.0236664E-03 at 50iterations finished qdiffx linear iterations at : 08:16:25 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 4.1861629E-05 9.0236664E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 08:16:26 3.562u 0.173s 0:04.01 93.0% 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 08:16:26 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5601 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: 1.618182 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): -16.78500 49.21500 ymin,ymax (A): 4.250000 68.83100 zmin,zma (A): -110.3780 -45.84200 x,y,z range (A): 66.00000 64.58100 64.53600 scale (grids/A): 1.618182 object centre (A): 16.21500 36.54050 -78.11000 number of atom coordinates read : 5601 total number of charged atoms : 5435 net assigned charge : -2.499965 assigned positive charge : 841.4996 centred at (gu) : 90.59982 93.47343 87.75070 assigned negative charge : -844.0068 centred at (gu) : 90.54704 93.39827 87.36982 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 115546 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49444 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 36043 mr = 79121 m= 3803 mr = 24522 m= 95 mr = 1830 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1793 time to turn everything in is 0.5500000 number of dielectric boundary points 50013 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 599 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 41546 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) : 0.5393940 object centre at (A) : 16.21500 36.54050 -78.11000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7714543E-02 2.1934193E-02 midg,1,midg; midg,igrid,midg -4.0944144E-03 -2.5466611E-03 1,midg,midg; igrid,midg,midg -5.9303027E-03 -1.2152020E-02 gauss-seidel spectral radius is 0.9984082 estimated iterations to convergence 199 setup time was (sec) 0.7800000 now iterating at: 08:16:27 rms-change max change #iterations 4.769514 164.9846 at 10iterations 2.095982 61.82872 at 20iterations 0.9221904 26.64475 at 30iterations 0.4071941 13.05384 at 40iterations 0.1795935 4.693744 at 50iterations 7.9125784E-02 2.324490 at 60iterations 3.4983713E-02 1.001325 at 70iterations 1.5453217E-02 0.4169979 at 80iterations 6.8590082E-03 0.1974351 at 90iterations 3.0453829E-03 9.3632698E-02 at 100iterations 1.3590476E-03 3.9245605E-02 at 110iterations 6.1604183E-04 1.8630981E-02 at 120iterations finished qdiffx linear iterations at : 08:16:34 total time elapsed so far: 8.050000 # loops : 120 mean,max change (kT/e) : 6.1604183E-04 1.8630981E-02 energy calculations done at 8.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.180000 DelPhi exited at 08:16:35 8.184u 0.187s 0:08.72 95.8% 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 08:16:35 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5601 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: 2.427273 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): -16.78500 49.21500 ymin,ymax (A): 4.250000 68.83100 zmin,zma (A): -110.3780 -45.84200 x,y,z range (A): 66.00000 64.58100 64.53600 scale (grids/A): 2.427273 object centre (A): 16.21500 36.54050 -78.11000 number of atom coordinates read : 5601 total number of charged atoms : 5435 net assigned charge : -2.499965 assigned positive charge : 841.4996 centred at (gu) : 90.89928 95.20969 86.62547 assigned negative charge : -844.0068 centred at (gu) : 90.82041 95.09734 86.05460 start vw surface at 0.1300000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 268579 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49444 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 124720 mr = 194136 m= 35377 mr = 97651 m= 5819 mr = 26270 m= 406 mr = 3819 m= 3 mr = 182 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 6004 time to turn everything in is 1.360000 number of dielectric boundary points 112846 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 42 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 43411 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) : 1.618182 object centre at (A) : 16.21500 36.54050 -78.11000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9576603 0.2543819 midg,1,midg; midg,igrid,midg -1.5621855E-02 1.5094753E-02 1,midg,midg; igrid,midg,midg -0.4546769 -3.9333235E-02 gauss-seidel spectral radius is 0.9992767 estimated iterations to convergence 293 setup time was (sec) 1.630000 now iterating at: 08:16:37 rms-change max change #iterations 12.43623 318.7613 at 10iterations 7.480478 160.1942 at 20iterations 4.476919 107.1608 at 30iterations 2.658758 51.79494 at 40iterations 1.567285 31.68472 at 50iterations 0.9233224 17.67703 at 60iterations 0.5431374 10.11486 at 70iterations 0.3177783 5.665860 at 80iterations 0.1860101 3.134232 at 90iterations 0.1088762 1.699363 at 100iterations 6.3463159E-02 1.198841 at 110iterations 3.6987375E-02 0.6217618 at 120iterations 2.1532487E-02 0.3940697 at 130iterations 1.2536385E-02 0.2034369 at 140iterations 7.2886134E-03 0.1216011 at 150iterations 4.2350469E-03 7.0102572E-02 at 160iterations 2.4643934E-03 4.1146278E-02 at 170iterations 1.4320797E-03 2.3859978E-02 at 180iterations finished qdiffx linear iterations at : 08:16:49 total time elapsed so far: 13.74000 # loops : 180 mean,max change (kT/e) : 1.4320797E-03 2.3859978E-02 energy calculations done at 13.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.87000 DelPhi exited at 08:16:49 13.877u 0.210s 0:14.34 98.1% 0+0k 0+0io 0pf+0w