Sat Oct 8 23:55:27 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 23:55:27 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 = 2584 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: 0.5935609 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): -27.55400 27.71100 ymin,ymax (A): 8.681000 52.28400 zmin,zma (A): -12.46400 47.51300 x,y,z range (A): 55.26500 43.60300 59.97700 scale (grids/A): 0.5935609 object centre (A): 7.8500748E-02 30.48250 17.52450 number of atom coordinates read : 2584 total number of charged atoms : 2448 net assigned charge : 12.50002 assigned positive charge : 376.0419 centred at (gu) : 90.25471 90.22138 90.14266 assigned negative charge : -363.5428 centred at (gu) : 90.26318 90.17592 90.14335 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6009 nv = 96 ne = 84 npr = 51835 no. pairs analyzed = 51835 no. exposed pairs = 3422 no. arc points = 24132 no. surface atoms = 1138 nbur = 1446 mkacc time = 9.0000004E-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 = 1.456000 m= 295 mr = 3039 m= 0 mr = 22 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 75 time to turn everything in is 0.2000000 number of dielectric boundary points 3243 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2410 ## 268 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7569 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2159889E-09 4.4517257E-09 midg,1,midg; midg,igrid,midg 2.9113025E-09 5.8820500E-09 1,midg,midg; igrid,midg,midg 4.3175108E-09 4.3327919E-09 gauss-seidel spectral radius is 0.9853171 estimated iterations to convergence 68 setup time was (sec) 0.3900000 now iterating at: 23:55:28 rms-change max change #iterations 9.8321885E-02 17.33646 at 10iterations 8.3045317E-03 1.304913 at 20iterations 1.0063028E-03 0.2045403 at 30iterations 2.4795523E-04 5.4033279E-02 at 40iterations 7.9057812E-05 1.7698288E-02 at 50iterations finished qdiffx linear iterations at : 23:55:31 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 7.9057812E-05 1.7698288E-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) 3.570000 DelPhi exited at 23:55:31 3.578u 0.201s 0:04.09 92.1% 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 23:55:31 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 = 2584 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: 1.780683 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): -27.55400 27.71100 ymin,ymax (A): 8.681000 52.28400 zmin,zma (A): -12.46400 47.51300 x,y,z range (A): 55.26500 43.60300 59.97700 scale (grids/A): 1.780683 object centre (A): 7.8500748E-02 30.48250 17.52450 number of atom coordinates read : 2584 total number of charged atoms : 2448 net assigned charge : 12.50002 assigned positive charge : 376.0419 centred at (gu) : 90.76378 90.66362 90.42730 assigned negative charge : -363.5428 centred at (gu) : 90.78945 90.52753 90.43000 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 66239 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24132 grid for indexing accessible points = 1.400000 m= 21924 mr = 44344 m= 2950 mr = 15286 m= 145 mr = 1644 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 2267 time to turn everything in is 0.3300000 number of dielectric boundary points 29943 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 215 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 19074 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) : 0.5935609 object centre at (A) : 7.8500748E-02 30.48250 17.52450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4239266E-02 1.6163895E-02 midg,1,midg; midg,igrid,midg 3.8757869E-03 1.8081062E-02 1,midg,midg; igrid,midg,midg 2.7626006E-02 3.1639319E-02 gauss-seidel spectral radius is 0.9984510 estimated iterations to convergence 202 setup time was (sec) 0.5600000 now iterating at: 23:55:32 rms-change max change #iterations 3.607074 167.0472 at 10iterations 1.598757 65.62621 at 20iterations 0.7116237 26.56165 at 30iterations 0.3169878 11.21964 at 40iterations 0.1409979 5.478882 at 50iterations 6.2852219E-02 2.383926 at 60iterations 2.7953943E-02 1.008698 at 70iterations 1.2561816E-02 0.4134967 at 80iterations 5.6580356E-03 0.1809883 at 90iterations 2.5771395E-03 8.7355614E-02 at 100iterations 1.2197017E-03 4.2304993E-02 at 110iterations 6.1060669E-04 2.6821136E-02 at 120iterations finished qdiffx linear iterations at : 23:55:39 total time elapsed so far: 7.930000 # loops : 120 mean,max change (kT/e) : 6.1060669E-04 2.6821136E-02 energy calculations done at 7.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 23:55:40 8.059u 0.219s 0:08.54 96.7% 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 Sat Oct 8 2011 at 23:55:40 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 = 2584 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: 2.671024 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): -27.55400 27.71100 ymin,ymax (A): 8.681000 52.28400 zmin,zma (A): -12.46400 47.51300 x,y,z range (A): 55.26500 43.60300 59.97700 scale (grids/A): 2.671024 object centre (A): 7.8500748E-02 30.48250 17.52450 number of atom coordinates read : 2584 total number of charged atoms : 2448 net assigned charge : 12.50002 assigned positive charge : 376.0419 centred at (gu) : 91.14546 90.99535 90.64067 assigned negative charge : -363.5428 centred at (gu) : 91.18402 90.79131 90.64505 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 153608 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24132 grid for indexing accessible points = 1.400000 m= 72625 mr = 108259 m= 23781 mr = 57606 m= 5010 mr = 18370 m= 614 mr = 3474 m= 31 mr = 367 m= 0 mr = 6 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 7441 time to turn everything in is 0.8200000 number of dielectric boundary points 67587 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 19578 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) : 1.780683 object centre at (A) : 7.8500748E-02 30.48250 17.52450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5811625 0.3250961 midg,1,midg; midg,igrid,midg 1.9968113E-02 0.2096745 1,midg,midg; igrid,midg,midg 0.3150062 0.3584808 gauss-seidel spectral radius is 0.9992122 estimated iterations to convergence 281 setup time was (sec) 1.070000 now iterating at: 23:55:41 rms-change max change #iterations 8.875203 296.6979 at 10iterations 5.145535 136.1923 at 20iterations 2.962310 62.65888 at 30iterations 1.697544 36.84872 at 40iterations 0.9696679 20.46196 at 50iterations 0.5530778 12.02526 at 60iterations 0.3146470 6.157185 at 70iterations 0.1786424 3.984776 at 80iterations 0.1013938 2.118495 at 90iterations 5.7383034E-02 1.240673 at 100iterations 3.2479901E-02 0.6352444 at 110iterations 1.8346112E-02 0.3703718 at 120iterations 1.0401157E-02 0.2282991 at 130iterations 5.8794976E-03 0.1280212 at 140iterations 3.3271245E-03 6.9068909E-02 at 150iterations 1.8772272E-03 3.8913727E-02 at 160iterations 1.0613590E-03 2.1320343E-02 at 170iterations 6.0055975E-04 1.1334419E-02 at 180iterations finished qdiffx linear iterations at : 23:55:53 total time elapsed so far: 12.86000 # loops : 180 mean,max change (kT/e) : 6.0055975E-04 1.1334419E-02 energy calculations done at 12.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.99000 DelPhi exited at 23:55:53 12.995u 0.250s 0:13.56 97.6% 0+0k 0+0io 0pf+0w