Mon Oct 10 16:23:19 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 Mon Oct 10 2011 at 16:23:19 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 = 2755 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: 0.5464984 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): 17.24800 68.73800 ymin,ymax (A): -63.45700 1.685000 zmin,zma (A): -41.85500 12.58700 x,y,z range (A): 51.49000 65.14200 54.44200 scale (grids/A): 0.5464984 object centre (A): 42.99300 -30.88600 -14.63400 number of atom coordinates read : 2755 total number of charged atoms : 2614 net assigned charge : 13.50002 assigned positive charge : 414.7844 centred at (gu) : 88.36074 88.93005 91.33559 assigned negative charge : -401.2855 centred at (gu) : 88.30394 88.98577 91.34142 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5419 nv = 96 ne = 84 npr = 52853 no. pairs analyzed = 52853 no. exposed pairs = 3716 no. arc points = 27777 no. surface atoms = 1255 nbur = 1500 mkacc time = 0.1200000 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= 215 mr = 2466 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3100000 number of dielectric boundary points 3160 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2876 ## 405 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7083 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4749733E-10 1.1312631E-09 midg,1,midg; midg,igrid,midg 1.5476304E-09 4.0171400E-10 1,midg,midg; igrid,midg,midg 7.4470918E-10 8.0691515E-10 gauss-seidel spectral radius is 0.9827337 estimated iterations to convergence 63 setup time was (sec) 0.5700000 now iterating at: 16:23:20 rms-change max change #iterations 6.9760777E-02 11.92603 at 10iterations 4.6115951E-03 0.7424240 at 20iterations 3.1006039E-04 6.2736511E-02 at 30iterations 2.1073784E-05 3.4790039E-03 at 40iterations 1.5160075E-06 2.8991699E-04 at 50iterations finished qdiffx linear iterations at : 16:23:23 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 1.5160075E-06 2.8991699E-04 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 16:23:23 3.545u 0.190s 0:04.02 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 Mon Oct 10 2011 at 16:23:23 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 = 2755 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: 1.639495 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): 17.24800 68.73800 ymin,ymax (A): -63.45700 1.685000 zmin,zma (A): -41.85500 12.58700 x,y,z range (A): 51.49000 65.14200 54.44200 scale (grids/A): 1.639495 object centre (A): 42.99300 -30.88600 -14.63400 number of atom coordinates read : 2755 total number of charged atoms : 2614 net assigned charge : 13.50002 assigned positive charge : 414.7844 centred at (gu) : 85.08138 86.78951 94.00603 assigned negative charge : -401.2855 centred at (gu) : 84.91174 86.95692 94.02428 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 59358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27777 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 17402 mr = 36956 m= 1686 mr = 11567 m= 48 mr = 730 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 703 time to turn everything in is 0.4600000 number of dielectric boundary points 29239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 363 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 19988 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) : 0.5464984 object centre at (A) : 42.99300 -30.88600 -14.63400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2452931E-02 1.4360894E-02 midg,1,midg; midg,igrid,midg 2.8505202E-02 -5.8747390E-03 1,midg,midg; igrid,midg,midg 1.0481728E-02 8.9348657E-03 gauss-seidel spectral radius is 0.9981877 estimated iterations to convergence 187 setup time was (sec) 0.7600000 now iterating at: 16:23:24 rms-change max change #iterations 3.173080 142.3050 at 10iterations 1.304840 52.56500 at 20iterations 0.5422820 22.30345 at 30iterations 0.2247079 8.981226 at 40iterations 9.3621425E-02 3.690455 at 50iterations 3.8933776E-02 1.534732 at 60iterations 1.6203064E-02 0.5808702 at 70iterations 6.7308326E-03 0.2973099 at 80iterations 2.7971270E-03 0.1053619 at 90iterations 1.1689259E-03 4.2926788E-02 at 100iterations 4.8538245E-04 1.9655228E-02 at 110iterations 2.0264422E-04 8.2969666E-03 at 120iterations finished qdiffx linear iterations at : 16:23:31 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 2.0264422E-04 8.2969666E-03 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 16:23:32 7.848u 0.238s 0:08.35 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 Mon Oct 10 2011 at 16:23:32 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 = 2755 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: 2.459243 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): 17.24800 68.73800 ymin,ymax (A): -63.45700 1.685000 zmin,zma (A): -41.85500 12.58700 x,y,z range (A): 51.49000 65.14200 54.44200 scale (grids/A): 2.459243 object centre (A): 42.99300 -30.88600 -14.63400 number of atom coordinates read : 2755 total number of charged atoms : 2614 net assigned charge : 13.50002 assigned positive charge : 414.7844 centred at (gu) : 82.62191 85.18403 96.00883 assigned negative charge : -401.2855 centred at (gu) : 82.36754 85.43529 96.03639 start vw surface at 0.1600000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 137506 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27777 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 59705 mr = 90849 m= 16702 mr = 46160 m= 2539 mr = 12125 m= 171 mr = 1531 m= 3 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 2444 time to turn everything in is 1.100000 number of dielectric boundary points 65898 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 20880 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) : 1.639495 object centre at (A) : 42.99300 -30.88600 -14.63400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1578111 0.2343539 midg,1,midg; midg,igrid,midg 0.4970725 -0.4838113 1,midg,midg; igrid,midg,midg 0.1807781 0.1112636 gauss-seidel spectral radius is 0.9991316 estimated iterations to convergence 268 setup time was (sec) 1.430000 now iterating at: 16:23:33 rms-change max change #iterations 8.147398 348.9045 at 10iterations 4.547446 114.6413 at 20iterations 2.518833 57.68932 at 30iterations 1.390355 34.93133 at 40iterations 0.7650275 17.95459 at 50iterations 0.4203645 8.701925 at 60iterations 0.2311906 5.194649 at 70iterations 0.1262674 2.862511 at 80iterations 6.9215491E-02 1.548299 at 90iterations 3.7910651E-02 0.8140278 at 100iterations 2.0701600E-02 0.4367301 at 110iterations 1.1348794E-02 0.2390289 at 120iterations 6.2044002E-03 0.1634808 at 130iterations 3.3981951E-03 7.6751709E-02 at 140iterations 1.8598499E-03 3.9884567E-02 at 150iterations 1.0177261E-03 1.9847870E-02 at 160iterations 5.5690791E-04 1.2302399E-02 at 170iterations 3.0424615E-04 6.5383911E-03 at 180iterations finished qdiffx linear iterations at : 16:23:45 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 3.0424615E-04 6.5383911E-03 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.84000 DelPhi exited at 16:23:45 12.846u 0.244s 0:13.37 97.8% 0+0k 0+0io 0pf+0w