Sun Oct 9 07:18:15 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 07:18:15 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2479 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: 0.5448507 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): -4.125000 42.11600 ymin,ymax (A): 35.82400 88.73800 zmin,zma (A): -3.218000 62.12100 x,y,z range (A): 46.24100 52.91400 65.33900 scale (grids/A): 0.5448507 object centre (A): 18.99550 62.28100 29.45150 number of atom coordinates read : 2479 total number of charged atoms : 2332 net assigned charge : -11.49998 assigned positive charge : 372.3360 centred at (gu) : 90.50787 88.68118 89.33825 assigned negative charge : -383.8364 centred at (gu) : 90.68587 88.35784 89.27764 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4871 nv = 96 ne = 84 npr = 49252 no. pairs analyzed = 49252 no. exposed pairs = 3437 no. arc points = 25025 no. surface atoms = 1153 nbur = 1326 mkacc time = 7.9999998E-02 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 = 1.568000 m= 195 mr = 2282 m= 0 mr = 13 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 2771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2511 ## 332 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6309 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1517411E-09 -2.7148198E-10 midg,1,midg; midg,igrid,midg -3.4694685E-09 7.5231849E-10 1,midg,midg; igrid,midg,midg 2.6815045E-10 -1.8626796E-09 gauss-seidel spectral radius is 0.9826041 estimated iterations to convergence 62 setup time was (sec) 0.3500000 now iterating at: 07:18:15 rms-change max change #iterations 6.6480406E-02 12.83825 at 10iterations 4.2170943E-03 1.023163 at 20iterations 2.8016907E-04 4.7806740E-02 at 30iterations 1.8131932E-05 3.3473969E-03 at 40iterations 1.2164847E-06 2.1982193E-04 at 50iterations finished qdiffx linear iterations at : 07:18:18 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.2164847E-06 2.1982193E-04 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 07:18:18 3.351u 0.187s 0:03.80 92.8% 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 07:18:18 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2479 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: 1.634552 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): -4.125000 42.11600 ymin,ymax (A): 35.82400 88.73800 zmin,zma (A): -3.218000 62.12100 x,y,z range (A): 46.24100 52.91400 65.33900 scale (grids/A): 1.634552 object centre (A): 18.99550 62.28100 29.45150 number of atom coordinates read : 2479 total number of charged atoms : 2332 net assigned charge : -11.49998 assigned positive charge : 372.3360 centred at (gu) : 91.52319 86.04303 88.01431 assigned negative charge : -383.8364 centred at (gu) : 92.05730 85.07315 87.83257 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 53573 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25025 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15763 mr = 33951 m= 1441 mr = 10522 m= 39 mr = 647 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 375 time to turn everything in is 0.2700000 number of dielectric boundary points 25693 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 260 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 17854 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) : 0.5448507 object centre at (A) : 18.99550 62.28100 29.45150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4242965E-02 2.8076326E-03 midg,1,midg; midg,igrid,midg -2.5543272E-02 3.7218235E-03 1,midg,midg; igrid,midg,midg -2.8946982E-03 -1.4723087E-02 gauss-seidel spectral radius is 0.9981382 estimated iterations to convergence 184 setup time was (sec) 0.4800000 now iterating at: 07:18:19 rms-change max change #iterations 3.027531 150.6809 at 10iterations 1.250608 52.46900 at 20iterations 0.5128956 22.98941 at 30iterations 0.2116669 8.347870 at 40iterations 8.6801752E-02 3.520729 at 50iterations 3.5737127E-02 1.434123 at 60iterations 1.4633301E-02 0.6279488 at 70iterations 6.0436968E-03 0.2485533 at 80iterations 2.4886855E-03 9.4047785E-02 at 90iterations 1.0236675E-03 4.1524410E-02 at 100iterations 4.2330276E-04 1.6839981E-02 at 110iterations 1.7371155E-04 6.8349838E-03 at 120iterations finished qdiffx linear iterations at : 07:18:26 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 1.7371155E-04 6.8349838E-03 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.500000 DelPhi exited at 07:18:26 7.505u 0.190s 0:07.94 96.8% 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 07:18:26 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2479 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: 2.451828 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): -4.125000 42.11600 ymin,ymax (A): 35.82400 88.73800 zmin,zma (A): -3.218000 62.12100 x,y,z range (A): 46.24100 52.91400 65.33900 scale (grids/A): 2.451828 object centre (A): 18.99550 62.28100 29.45150 number of atom coordinates read : 2479 total number of charged atoms : 2332 net assigned charge : -11.49998 assigned positive charge : 372.3360 centred at (gu) : 92.28458 84.06459 87.02139 assigned negative charge : -383.8364 centred at (gu) : 93.08584 82.60969 86.74878 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 124128 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25025 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 54987 mr = 83352 m= 14487 mr = 42563 m= 2119 mr = 10489 m= 142 mr = 1317 m= 2 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 1289 time to turn everything in is 0.6400000 number of dielectric boundary points 58084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 18640 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) : 1.634552 object centre at (A) : 18.99550 62.28100 29.45150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9513722 2.3490803E-02 midg,1,midg; midg,igrid,midg -0.3380083 6.9581501E-02 1,midg,midg; igrid,midg,midg -4.3829784E-02 -0.1886484 gauss-seidel spectral radius is 0.9991140 estimated iterations to convergence 265 setup time was (sec) 0.8700000 now iterating at: 07:18:27 rms-change max change #iterations 7.925961 273.2011 at 10iterations 4.366539 183.2346 at 20iterations 2.416270 67.22241 at 30iterations 1.328675 33.11397 at 40iterations 0.7313413 17.59921 at 50iterations 0.4015695 9.906757 at 60iterations 0.2194097 4.975436 at 70iterations 0.1199650 2.908760 at 80iterations 6.5241568E-02 1.635858 at 90iterations 3.5660464E-02 0.8073730 at 100iterations 1.9406369E-02 0.4629440 at 110iterations 1.0564178E-02 0.2402492 at 120iterations 5.7634246E-03 0.1367607 at 130iterations 3.1363477E-03 7.3305368E-02 at 140iterations 1.7046839E-03 3.9503813E-02 at 150iterations 9.2767749E-04 2.0231247E-02 at 160iterations 5.0503388E-04 1.2159348E-02 at 170iterations 2.7512008E-04 6.2255859E-03 at 180iterations finished qdiffx linear iterations at : 07:18:38 total time elapsed so far: 11.72000 # loops : 180 mean,max change (kT/e) : 2.7512008E-04 6.2255859E-03 energy calculations done at 11.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.85000 DelPhi exited at 07:18:39 11.851u 0.199s 0:12.41 97.0% 0+0k 0+0io 0pf+0w