Sat Oct 8 11:41:01 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 Sat Oct 8 2011 at 11:41:01 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 = 2551 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: 0.6110853 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): 17.70700 75.96400 ymin,ymax (A): 3.397000 55.05400 zmin,zma (A): 11.16900 66.73100 x,y,z range (A): 58.25700 51.65700 55.56200 scale (grids/A): 0.6110853 object centre (A): 46.83550 29.22550 38.95000 number of atom coordinates read : 2551 total number of charged atoms : 2403 net assigned charge : -1.999992 assigned positive charge : 370.0657 centred at (gu) : 93.73590 89.62007 90.13144 assigned negative charge : -372.0664 centred at (gu) : 93.64726 89.56076 90.14966 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6312 nv = 96 ne = 84 npr = 51958 no. pairs analyzed = 51958 no. exposed pairs = 3228 no. arc points = 23058 no. surface atoms = 1098 nbur = 1453 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 288 mr = 3287 m= 3 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3296 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2337 ## 256 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7764 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7542825E-10 -2.3110527E-09 midg,1,midg; midg,igrid,midg -4.6216697E-09 1.3492212E-09 1,midg,midg; igrid,midg,midg -2.4979090E-09 6.9656387E-09 gauss-seidel spectral radius is 0.9861354 estimated iterations to convergence 70 setup time was (sec) 0.3700000 now iterating at: 11:41:02 rms-change max change #iterations 0.1180467 18.19589 at 10iterations 1.0368370E-02 1.690840 at 20iterations 9.2510571E-04 0.1694012 at 30iterations 8.3496634E-05 1.3496399E-02 at 40iterations 8.5305173E-06 1.4934540E-03 at 50iterations finished qdiffx linear iterations at : 11:41:04 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 8.5305173E-06 1.4934540E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 11:41:05 3.360u 0.181s 0:03.89 91.0% 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 Sat Oct 8 2011 at 11:41:05 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 = 2551 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: 1.833256 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): 17.70700 75.96400 ymin,ymax (A): 3.397000 55.05400 zmin,zma (A): 11.16900 66.73100 x,y,z range (A): 58.25700 51.65700 55.56200 scale (grids/A): 1.833256 object centre (A): 46.83550 29.22550 38.95000 number of atom coordinates read : 2551 total number of charged atoms : 2403 net assigned charge : -1.999992 assigned positive charge : 370.0657 centred at (gu) : 101.2069 88.85960 90.39382 assigned negative charge : -372.0664 centred at (gu) : 100.9416 88.68203 90.44865 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 68053 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23058 grid for indexing accessible points = 1.400000 m= 23226 mr = 45563 m= 3301 mr = 16758 m= 128 mr = 1931 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 30427 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 133 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 18790 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) : 0.6110853 object centre at (A) : 46.83550 29.22550 38.95000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0917985E-02 -2.2222415E-02 midg,1,midg; midg,igrid,midg 8.8523859E-03 -4.1560322E-04 1,midg,midg; igrid,midg,midg -1.3259432E-02 3.3740837E-02 gauss-seidel spectral radius is 0.9985175 estimated iterations to convergence 206 setup time was (sec) 0.5700000 now iterating at: 11:41:06 rms-change max change #iterations 3.810087 220.7432 at 10iterations 1.723683 75.45738 at 20iterations 0.7794535 26.04330 at 30iterations 0.3530245 11.74390 at 40iterations 0.1601374 5.247057 at 50iterations 7.2788790E-02 2.358463 at 60iterations 3.2971609E-02 1.071463 at 70iterations 1.4911970E-02 0.4904366 at 80iterations 6.7714159E-03 0.2300568 at 90iterations 3.0667023E-03 0.1001358 at 100iterations 1.3951530E-03 4.7146797E-02 at 110iterations 6.3307368E-04 2.2000313E-02 at 120iterations finished qdiffx linear iterations at : 11:41:13 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 6.3307368E-04 2.2000313E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 11:41:13 7.718u 0.190s 0:08.39 94.1% 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 Sat Oct 8 2011 at 11:41:13 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 = 2551 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: 2.749884 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): 17.70700 75.96400 ymin,ymax (A): 3.397000 55.05400 zmin,zma (A): 11.16900 66.73100 x,y,z range (A): 58.25700 51.65700 55.56200 scale (grids/A): 2.749884 object centre (A): 46.83550 29.22550 38.95000 number of atom coordinates read : 2551 total number of charged atoms : 2403 net assigned charge : -1.999992 assigned positive charge : 370.0657 centred at (gu) : 106.8102 88.28938 90.59052 assigned negative charge : -372.0664 centred at (gu) : 106.4123 88.02293 90.67300 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 157174 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23058 grid for indexing accessible points = 1.400000 m= 75978 mr = 110850 m= 26611 mr = 61078 m= 5698 mr = 21043 m= 626 mr = 4164 m= 28 mr = 359 m= 0 mr = 3 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8600000 number of dielectric boundary points 68618 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 19220 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) : 1.833256 object centre at (A) : 46.83550 29.22550 38.95000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1446043 -0.2812904 midg,1,midg; midg,igrid,midg 0.2267013 1.5553664E-02 1,midg,midg; igrid,midg,midg -7.6714814E-02 0.5487542 gauss-seidel spectral radius is 0.9992316 estimated iterations to convergence 285 setup time was (sec) 1.090000 now iterating at: 11:41:15 rms-change max change #iterations 9.181630 299.7505 at 10iterations 5.326949 130.9873 at 20iterations 3.078713 67.17914 at 30iterations 1.768010 36.66152 at 40iterations 1.012784 21.25800 at 50iterations 0.5776401 13.87463 at 60iterations 0.3298689 6.483852 at 70iterations 0.1883508 3.721185 at 80iterations 0.1070481 2.006709 at 90iterations 6.0973644E-02 1.119635 at 100iterations 3.4668222E-02 0.6559134 at 110iterations 1.9738242E-02 0.3855820 at 120iterations 1.1229820E-02 0.2212982 at 130iterations 6.3914228E-03 0.1223850 at 140iterations 3.6381464E-03 7.2318554E-02 at 150iterations 2.0721725E-03 4.3373108E-02 at 160iterations 1.1810556E-03 2.4292946E-02 at 170iterations 6.7634089E-04 1.2938976E-02 at 180iterations finished qdiffx linear iterations at : 11:41:26 total time elapsed so far: 12.29000 # loops : 180 mean,max change (kT/e) : 6.7634089E-04 1.2938976E-02 energy calculations done at 12.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.42000 DelPhi exited at 11:41:26 12.424u 0.211s 0:12.95 97.5% 0+0k 0+0io 0pf+0w