Wed Feb 15 09:01:23 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+sph_thinner.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 Wed Feb 15 2012 at 09:01:23 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 = 5576 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: 0.5310025 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): 15.25800 78.55500 ymin,ymax (A): 10.95500 76.69000 zmin,zma (A): 8.405999 75.44901 x,y,z range (A): 63.29700 65.73500 67.04301 scale (grids/A): 0.5310025 object centre (A): 46.90650 43.82250 41.92750 number of atom coordinates read : 5576 total number of charged atoms : 5404 net assigned charge : 1.500026 assigned positive charge : 850.9199 centred at (gu) : 89.74300 90.56958 90.39426 assigned negative charge : -849.4263 centred at (gu) : 89.77613 90.57764 90.42142 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 9584 nv = 96 ne = 84 npr = 116529 no. pairs analyzed = 116529 no. exposed pairs = 6684 no. arc points = 45852 no. surface atoms = 2237 nbur = 3339 mkacc time = 0.3000000 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 = 1.624000 m= 375 mr = 5130 m= 0 mr = 13 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 4816 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4565 ## 616 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 13154 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2142405E-10 -1.5877452E-10 midg,1,midg; midg,igrid,midg 9.4435119E-11 -7.4069067E-12 1,midg,midg; igrid,midg,midg 3.0662797E-10 -1.7394043E-10 gauss-seidel spectral radius is 0.9819025 estimated iterations to convergence 61 setup time was (sec) 0.8700000 now iterating at: 09:01:24 rms-change max change #iterations 8.8655904E-02 13.52564 at 10iterations 6.9373087E-03 1.197853 at 20iterations 1.1738645E-03 0.2773895 at 30iterations 3.2850765E-04 6.7886353E-02 at 40iterations 1.1505016E-04 1.7585754E-02 at 50iterations finished qdiffx linear iterations at : 09:01:29 total time elapsed so far: 5.090000 # loops : 50 mean,max change (kT/e) : 1.1505016E-04 1.7585754E-02 energy calculations done at 5.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.260000 DelPhi exited at 09:01:29 5.268u 0.414s 0:06.04 93.8% 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 Wed Feb 15 2012 at 09:01:29 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 = 5576 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: 1.593007 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): 15.25800 78.55500 ymin,ymax (A): 10.95500 76.69000 zmin,zma (A): 8.405999 75.44901 x,y,z range (A): 63.29700 65.73500 67.04301 scale (grids/A): 1.593007 object centre (A): 46.90650 43.82250 41.92750 number of atom coordinates read : 5576 total number of charged atoms : 5404 net assigned charge : 1.500026 assigned positive charge : 850.9199 centred at (gu) : 89.22687 91.70699 91.18097 assigned negative charge : -849.4263 centred at (gu) : 89.32817 91.73231 91.26413 start vw surface at 0.1900000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 109056 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45852 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 32899 mr = 76544 m= 3092 mr = 22344 m= 70 mr = 1409 m= 0 mr = 2 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 1113 time to turn everything in is 0.8900000 number of dielectric boundary points 44818 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 605 ## 11 charges are in solution ## iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 41116 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) : 0.5310025 object centre at (A) : 46.90650 43.82250 41.92750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0054320E-02 8.8775558E-03 midg,1,midg; midg,igrid,midg 1.2685644E-02 -4.1935924E-03 1,midg,midg; igrid,midg,midg 4.5312173E-03 -6.8646357E-03 gauss-seidel spectral radius is 0.9983302 estimated iterations to convergence 194 setup time was (sec) 1.200000 now iterating at: 09:01:31 rms-change max change #iterations 4.562096 181.3449 at 10iterations 1.973583 59.15325 at 20iterations 0.8502095 24.38104 at 30iterations 0.3690607 10.25769 at 40iterations 0.1598972 4.584642 at 50iterations 6.9156617E-02 1.955086 at 60iterations 3.0114369E-02 0.8737984 at 70iterations 1.3152506E-02 0.3832703 at 80iterations 5.8068135E-03 0.1815948 at 90iterations 2.5958165E-03 9.2597961E-02 at 100iterations 1.1997010E-03 4.0191650E-02 at 110iterations 5.9091422E-04 2.1018982E-02 at 120iterations finished qdiffx linear iterations at : 09:01:41 total time elapsed so far: 11.78000 # loops : 120 mean,max change (kT/e) : 5.9091422E-04 2.1018982E-02 energy calculations done at 11.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.93000 DelPhi exited at 09:01:42 11.939u 0.476s 0:12.76 97.1% 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 Wed Feb 15 2012 at 09:01:42 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 = 5576 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: 2.389511 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): 15.25800 78.55500 ymin,ymax (A): 10.95500 76.69000 zmin,zma (A): 8.405999 75.44901 x,y,z range (A): 63.29700 65.73500 67.04301 scale (grids/A): 2.389511 object centre (A): 46.90650 43.82250 41.92750 number of atom coordinates read : 5576 total number of charged atoms : 5404 net assigned charge : 1.500026 assigned positive charge : 850.9199 centred at (gu) : 88.84003 92.55991 91.77115 assigned negative charge : -849.4263 centred at (gu) : 88.99201 92.59853 91.89629 start vw surface at 0.1900000 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 254528 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45852 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 115352 mr = 188084 m= 31391 mr = 90752 m= 4554 mr = 23206 m= 234 mr = 2823 m= 2 mr = 80 m= 2 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.360000 no. cavity mid-points inaccessible to solvent = 3614 time to turn everything in is 2.220000 number of dielectric boundary points 101118 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 49 iepsmp to db, and charging done at 2.390000 number of grid points assigned charge 43167 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) : 1.593007 object centre at (A) : 46.90650 43.82250 41.92750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2395363 9.8739631E-02 midg,1,midg; midg,igrid,midg 0.1513476 -9.3035311E-02 1,midg,midg; igrid,midg,midg 4.9083754E-02 -0.1833821 gauss-seidel spectral radius is 0.9992405 estimated iterations to convergence 286 setup time was (sec) 2.600000 now iterating at: 09:01:45 rms-change max change #iterations 12.16798 371.7266 at 10iterations 7.245098 155.1266 at 20iterations 4.281085 88.03625 at 30iterations 2.514255 53.98445 at 40iterations 1.470136 33.35840 at 50iterations 0.8562374 17.85317 at 60iterations 0.4975363 8.896072 at 70iterations 0.2881939 6.628416 at 80iterations 0.1666569 3.123222 at 90iterations 9.6155562E-02 1.818130 at 100iterations 5.5518921E-02 1.120689 at 110iterations 3.1972408E-02 0.6082191 at 120iterations 1.8435046E-02 0.3197079 at 130iterations 1.0648569E-02 0.1870365 at 140iterations 6.1696004E-03 0.1194744 at 150iterations 3.5822096E-03 6.8441972E-02 at 160iterations 2.1014200E-03 3.8797379E-02 at 170iterations 1.2547176E-03 2.2704005E-02 at 180iterations finished qdiffx linear iterations at : 09:02:04 total time elapsed so far: 21.35000 # loops : 180 mean,max change (kT/e) : 1.2547176E-03 2.2704005E-02 energy calculations done at 21.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.51000 DelPhi exited at 09:02:04 21.514u 0.480s 0:22.28 98.6% 0+0k 0+0io 0pf+0w