Sun Oct 9 16:58:52 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 16:58:52 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 = 4747 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: 0.5135084 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): 3.229000 67.30600 ymin,ymax (A): -0.8649999 54.17100 zmin,zma (A): -35.96100 33.36600 x,y,z range (A): 64.07700 55.03600 69.32700 scale (grids/A): 0.5135084 object centre (A): 35.26750 26.65300 -1.297501 number of atom coordinates read : 4747 total number of charged atoms : 4592 net assigned charge : 7.500048 assigned positive charge : 718.1699 centred at (gu) : 89.85356 90.59117 91.17284 assigned negative charge : -710.6746 centred at (gu) : 89.93028 90.66740 91.06808 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7840 nv = 96 ne = 84 npr = 96737 no. pairs analyzed = 96737 no. exposed pairs = 5651 no. arc points = 38846 no. surface atoms = 1906 nbur = 2841 mkacc time = 0.1600000 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 = 1.680000 m= 263 mr = 4251 m= 0 mr = 7 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3100000 number of dielectric boundary points 3845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3897 ## 590 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 10599 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3930049E-10 5.7252453E-10 midg,1,midg; midg,igrid,midg 2.9004585E-10 -1.2558450E-10 1,midg,midg; igrid,midg,midg 3.5317946E-10 -1.0352388E-10 gauss-seidel spectral radius is 0.9805956 estimated iterations to convergence 59 setup time was (sec) 0.5000000 now iterating at: 16:58:52 rms-change max change #iterations 7.1199790E-02 11.23302 at 10iterations 5.6284540E-03 0.8307362 at 20iterations 1.3831127E-03 0.2185421 at 30iterations 5.4141355E-04 9.1876984E-02 at 40iterations 2.2131650E-04 3.8755417E-02 at 50iterations finished qdiffx linear iterations at : 16:58:55 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 2.2131650E-04 3.8755417E-02 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 16:58:56 3.562u 0.182s 0:04.01 93.2% 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 16:58:56 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 = 4747 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: 1.540525 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): 3.229000 67.30600 ymin,ymax (A): -0.8649999 54.17100 zmin,zma (A): -35.96100 33.36600 x,y,z range (A): 64.07700 55.03600 69.32700 scale (grids/A): 1.540525 object centre (A): 35.26750 26.65300 -1.297501 number of atom coordinates read : 4747 total number of charged atoms : 4592 net assigned charge : 7.500048 assigned positive charge : 718.1699 centred at (gu) : 89.55933 91.77221 93.51721 assigned negative charge : -710.6746 centred at (gu) : 89.79041 92.00155 93.20407 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 89399 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38846 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25341 mr = 62843 m= 2002 mr = 17017 m= 38 mr = 900 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 372 time to turn everything in is 0.4300000 number of dielectric boundary points 36020 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 556 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 34563 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) : 0.5135084 object centre at (A) : 35.26750 26.65300 -1.297501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3831997E-02 3.5701334E-02 midg,1,midg; midg,igrid,midg 9.0859048E-03 -1.9467081E-03 1,midg,midg; igrid,midg,midg 2.2737466E-02 -2.1977820E-03 gauss-seidel spectral radius is 0.9981237 estimated iterations to convergence 183 setup time was (sec) 0.6400000 now iterating at: 16:58:57 rms-change max change #iterations 3.788980 144.2473 at 10iterations 1.552080 60.61399 at 20iterations 0.6424017 19.52112 at 30iterations 0.2633236 8.410450 at 40iterations 0.1091497 4.204788 at 50iterations 4.5020100E-02 1.413345 at 60iterations 1.8831922E-02 0.5512886 at 70iterations 8.1014782E-03 0.2683964 at 80iterations 3.7483664E-03 0.1417971 at 90iterations 1.9567546E-03 7.0224762E-02 at 100iterations 1.1804582E-03 4.4187546E-02 at 110iterations 7.8959658E-04 2.7637482E-02 at 120iterations finished qdiffx linear iterations at : 16:59:04 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 7.8959658E-04 2.7637482E-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) 7.970000 DelPhi exited at 16:59:04 7.977u 0.213s 0:08.46 96.6% 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 16:59:04 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 = 4747 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: 2.310788 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): 3.229000 67.30600 ymin,ymax (A): -0.8649999 54.17100 zmin,zma (A): -35.96100 33.36600 x,y,z range (A): 64.07700 55.03600 69.32700 scale (grids/A): 2.310788 object centre (A): 35.26750 26.65300 -1.297501 number of atom coordinates read : 4747 total number of charged atoms : 4592 net assigned charge : 7.500048 assigned positive charge : 718.1699 centred at (gu) : 89.33866 92.65794 95.27524 assigned negative charge : -710.6746 centred at (gu) : 89.68544 93.00243 94.80618 start vw surface at 0.1300000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 208884 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38846 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 91851 mr = 154260 m= 22356 mr = 72463 m= 2909 mr = 16363 m= 147 mr = 1825 m= 4 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 1275 time to turn everything in is 1.050000 number of dielectric boundary points 81183 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 36645 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) : 1.540525 object centre at (A) : 35.26750 26.65300 -1.297501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2393965 0.6185468 midg,1,midg; midg,igrid,midg 0.1281801 -3.9877061E-02 1,midg,midg; igrid,midg,midg 0.4099408 -1.3773228E-03 gauss-seidel spectral radius is 0.9991598 estimated iterations to convergence 272 setup time was (sec) 1.290000 now iterating at: 16:59:06 rms-change max change #iterations 10.22305 272.5701 at 10iterations 5.867331 128.0441 at 20iterations 3.340509 71.51453 at 30iterations 1.886353 38.70870 at 40iterations 1.062772 21.81641 at 50iterations 0.5966886 13.07010 at 60iterations 0.3343758 6.995793 at 70iterations 0.1866350 3.694439 at 80iterations 0.1042433 1.932587 at 90iterations 5.8174361E-02 1.100967 at 100iterations 3.2380935E-02 0.6442566 at 110iterations 1.8065868E-02 0.3725891 at 120iterations 1.0089302E-02 0.2084198 at 130iterations 5.6621637E-03 0.1099594 at 140iterations 3.1922404E-03 5.7186127E-02 at 150iterations 1.8241148E-03 3.6308289E-02 at 160iterations 1.0652744E-03 2.4848938E-02 at 170iterations 6.4638536E-04 1.2493134E-02 at 180iterations finished qdiffx linear iterations at : 16:59:17 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 6.4638536E-04 1.2493134E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 16:59:18 12.943u 0.191s 0:13.46 97.5% 0+0k 0+0io 0pf+0w