Thu Jan 19 13:32:14 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.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 Thu Jan 19 2012 at 13:32:14 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6928 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4313008 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): -5.503000 77.03800 ymin,ymax (A): -1.053000 75.41900 zmin,zma (A): 159.2140 228.3830 x,y,z range (A): 82.54100 76.47200 69.16901 scale (grids/A): 0.4313008 object centre (A): 35.76750 37.18300 193.7985 number of atom coordinates read : 6928 total number of charged atoms : 6757 net assigned charge : 0.2000304 assigned positive charge : 1052.503 centred at (gu) : 88.99567 89.99706 89.51878 assigned negative charge : -1052.311 centred at (gu) : 89.00697 90.03591 89.49297 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7586 nv = 96 ne = 84 npr = 139601 no. pairs analyzed = 139601 no. exposed pairs = 9038 no. arc points = 61749 no. surface atoms = 3024 nbur = 3904 mkacc time = 0.2400000 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 = 1.932000 m= 193 mr = 3543 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5101 ## 1033 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10528 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0331267E-12 1.5672898E-12 midg,1,midg; midg,igrid,midg 2.7147425E-12 -2.6554228E-12 1,midg,midg; igrid,midg,midg 1.1273685E-12 -5.3995523E-13 gauss-seidel spectral radius is 0.9727288 estimated iterations to convergence 51 setup time was (sec) 0.6300000 now iterating at: 13:32:15 rms-change max change #iterations 3.0598508E-02 5.736227 at 10iterations 2.0474128E-03 0.3446388 at 20iterations 5.9797603E-04 7.5178146E-02 at 30iterations 2.0289568E-04 2.8687000E-02 at 40iterations 6.9416325E-05 1.0908604E-02 at 50iterations finished qdiffx linear iterations at : 13:32:20 total time elapsed so far: 3.620000 # loops : 50 mean,max change (kT/e) : 6.9416325E-05 1.0908604E-02 energy calculations done at 3.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.780000 DelPhi exited at 13:32:21 3.780u 0.173s 0:06.87 57.4% 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 Thu Jan 19 2012 at 13:32:21 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6928 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.293902 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): -5.503000 77.03800 ymin,ymax (A): -1.053000 75.41900 zmin,zma (A): 159.2140 228.3830 x,y,z range (A): 82.54100 76.47200 69.16901 scale (grids/A): 1.293902 object centre (A): 35.76750 37.18300 193.7985 number of atom coordinates read : 6928 total number of charged atoms : 6757 net assigned charge : 0.2000304 assigned positive charge : 1052.503 centred at (gu) : 86.98465 89.98920 88.55445 assigned negative charge : -1052.311 centred at (gu) : 87.02068 90.10739 88.47867 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 88680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 61749 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 20512 mr = 58306 m= 1034 mr = 11902 m= 6 mr = 228 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 478 time to turn everything in is 0.4800000 number of dielectric boundary points 39796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1106 ## 43 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 46956 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) : 0.4313008 object centre at (A) : 35.76750 37.18300 193.7985 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4448865E-04 -2.5277590E-05 midg,1,midg; midg,igrid,midg -8.2579075E-04 -4.4110715E-03 1,midg,midg; igrid,midg,midg 1.2754741E-03 3.5327259E-03 gauss-seidel spectral radius is 0.9974365 estimated iterations to convergence 157 setup time was (sec) 0.7000000 now iterating at: 13:32:23 rms-change max change #iterations 3.092146 129.4512 at 10iterations 1.095294 36.37346 at 20iterations 0.3859815 14.91931 at 30iterations 0.1372353 4.573048 at 40iterations 4.8864216E-02 1.721091 at 50iterations 1.7429056E-02 0.6638069 at 60iterations 6.3345721E-03 0.2123299 at 70iterations 2.4563705E-03 8.1249237E-02 at 80iterations 1.0916834E-03 3.6743164E-02 at 90iterations 5.8454182E-04 1.8577576E-02 at 100iterations 3.5994773E-04 1.0421753E-02 at 110iterations 2.3465541E-04 6.4873695E-03 at 120iterations finished qdiffx linear iterations at : 13:32:32 total time elapsed so far: 8.440000 # loops : 120 mean,max change (kT/e) : 2.3465541E-04 6.4873695E-03 energy calculations done at 8.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.610000 DelPhi exited at 13:32:33 8.614u 0.202s 0:11.73 75.1% 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 Thu Jan 19 2012 at 13:32:33 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6928 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 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: 1.940854 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): -5.503000 77.03800 ymin,ymax (A): -1.053000 75.41900 zmin,zma (A): 159.2140 228.3830 x,y,z range (A): 82.54100 76.47200 69.16901 scale (grids/A): 1.940854 object centre (A): 35.76750 37.18300 193.7985 number of atom coordinates read : 6928 total number of charged atoms : 6757 net assigned charge : 0.2000304 assigned positive charge : 1052.503 centred at (gu) : 85.47652 89.98347 87.83099 assigned negative charge : -1052.311 centred at (gu) : 85.53087 90.16085 87.71783 start vw surface at 0.1700000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 208381 reading accessible surface arcs data from file ARCDAT no. of arc points read = 61749 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 79776 mr = 145915 m= 14198 mr = 58461 m= 1037 mr = 8817 m= 12 mr = 389 m= 0 mr = 0 time to grow re-entrant surface = 0.5899999 no. cavity mid-points inaccessible to solvent = 1551 time to turn everything in is 1.070000 number of dielectric boundary points 89822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 331 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 53327 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) : 1.293902 object centre at (A) : 35.76750 37.18300 193.7985 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7734760E-04 -7.5046332E-03 midg,1,midg; midg,igrid,midg -3.7793506E-02 -7.7284023E-02 1,midg,midg; igrid,midg,midg 0.1417660 0.1578306 gauss-seidel spectral radius is 0.9989926 estimated iterations to convergence 249 setup time was (sec) 1.330000 now iterating at: 13:32:34 rms-change max change #iterations 9.541101 249.8600 at 10iterations 5.181363 134.7151 at 20iterations 2.786563 71.09663 at 30iterations 1.488942 33.79338 at 40iterations 0.7920278 18.24914 at 50iterations 0.4203548 9.699522 at 60iterations 0.2227864 5.059879 at 70iterations 0.1174240 2.384674 at 80iterations 6.1946344E-02 1.386863 at 90iterations 3.2632157E-02 0.8449419 at 100iterations 1.7194606E-02 0.3378086 at 110iterations 9.0230461E-03 0.2012844 at 120iterations 4.7496231E-03 0.1033173 at 130iterations 2.4905901E-03 5.3466797E-02 at 140iterations 1.3081342E-03 2.7556419E-02 at 150iterations 6.8867864E-04 1.3065040E-02 at 160iterations 3.6216812E-04 7.3776245E-03 at 170iterations 1.9130019E-04 3.8223267E-03 at 180iterations finished qdiffx linear iterations at : 13:32:59 total time elapsed so far: 13.68000 # loops : 180 mean,max change (kT/e) : 1.9130019E-04 3.8223267E-03 energy calculations done at 13.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.81000 DelPhi exited at 13:33:00 13.808u 0.248s 0:27.48 51.0% 0+0k 0+0io 0pf+0w