Mon Oct 10 13:57:53 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 13:57:53 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2110 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7495368 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): 9.095000 56.59100 ymin,ymax (A): -9.289001 35.88800 zmin,zma (A): -2.933000 44.49300 x,y,z range (A): 47.49600 45.17700 47.42600 scale (grids/A): 0.7495368 object centre (A): 32.84300 13.29950 20.78000 number of atom coordinates read : 2110 total number of charged atoms : 1971 net assigned charge : -5.999980 assigned positive charge : 315.8319 centred at (gu) : 89.16025 90.81013 89.74673 assigned negative charge : -321.8320 centred at (gu) : 89.19157 90.87562 89.91659 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 8244 nv = 96 ne = 84 npr = 43428 no. pairs analyzed = 43428 no. exposed pairs = 2688 no. arc points = 18893 no. surface atoms = 910 nbur = 1200 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 593 mr = 4620 m= 2 mr = 128 m= 0 mr = 0 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 4091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1524 ## 123 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 8548 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.1369144E-08 -3.2731924E-07 midg,1,midg; midg,igrid,midg -4.3176339E-08 -2.4486516E-07 1,midg,midg; igrid,midg,midg -1.0521878E-07 -1.4479920E-07 gauss-seidel spectral radius is 0.9907237 estimated iterations to convergence 84 setup time was (sec) 0.3500000 now iterating at: 13:57:54 rms-change max change #iterations 0.2595121 35.55430 at 10iterations 3.5380878E-02 4.080748 at 20iterations 4.8642894E-03 0.5813236 at 30iterations 6.9215056E-04 7.5899124E-02 at 40iterations 9.4049276E-05 1.4535904E-02 at 50iterations finished qdiffx linear iterations at : 13:57:57 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 9.4049276E-05 1.4535904E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 13:57:57 3.327u 0.183s 0:03.91 89.5% 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 13:57:57 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2110 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.248610 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): 9.095000 56.59100 ymin,ymax (A): -9.289001 35.88800 zmin,zma (A): -2.933000 44.49300 x,y,z range (A): 47.49600 45.17700 47.42600 scale (grids/A): 2.248610 object centre (A): 32.84300 13.29950 20.78000 number of atom coordinates read : 2110 total number of charged atoms : 1971 net assigned charge : -5.999980 assigned positive charge : 315.8319 centred at (gu) : 87.48086 92.43031 89.23991 assigned negative charge : -321.8320 centred at (gu) : 87.57471 92.62686 89.74979 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 86202 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18893 grid for indexing accessible points = 1.400000 m= 35398 mr = 59914 m= 7880 mr = 27081 m= 883 mr = 5495 m= 21 mr = 490 m= 0 mr = 3 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 37401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 15710 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) : 0.7495368 object centre at (A) : 32.84300 13.29950 20.78000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8079124E-03 -0.1263901 midg,1,midg; midg,igrid,midg -3.3766262E-02 -4.7368988E-02 1,midg,midg; igrid,midg,midg -1.0218304E-02 1.4258922E-03 gauss-seidel spectral radius is 0.9989479 estimated iterations to convergence 244 setup time was (sec) 0.6400000 now iterating at: 13:57:58 rms-change max change #iterations 5.223273 213.7820 at 10iterations 2.658583 79.81984 at 20iterations 1.367589 43.49776 at 30iterations 0.7016522 19.35644 at 40iterations 0.3598234 11.87257 at 50iterations 0.1848390 5.123013 at 60iterations 9.4916448E-02 2.520985 at 70iterations 4.8783615E-02 1.385485 at 80iterations 2.5019856E-02 0.6548042 at 90iterations 1.2867126E-02 0.3714237 at 100iterations 6.5909186E-03 0.1787910 at 110iterations 3.3900763E-03 9.5747948E-02 at 120iterations finished qdiffx linear iterations at : 13:58:05 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 3.3900763E-03 9.5747948E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 13:58:06 7.836u 0.217s 0:08.35 96.2% 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 Mon Oct 10 2011 at 13:58:06 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2110 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.372916 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): 9.095000 56.59100 ymin,ymax (A): -9.289001 35.88800 zmin,zma (A): -2.933000 44.49300 x,y,z range (A): 47.49600 45.17700 47.42600 scale (grids/A): 3.372916 object centre (A): 32.84300 13.29950 20.78000 number of atom coordinates read : 2110 total number of charged atoms : 1971 net assigned charge : -5.999980 assigned positive charge : 315.8319 centred at (gu) : 86.22125 93.64536 88.85984 assigned negative charge : -321.8320 centred at (gu) : 86.36206 93.94028 89.62463 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 198294 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18893 grid for indexing accessible points = 1.400000 m= 107423 mr = 143958 m= 47326 mr = 89487 m= 15208 mr = 39396 m= 3449 mr = 12183 m= 479 mr = 2622 m= 16 mr = 314 m= 0 mr = 5 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.340000 number of dielectric boundary points 84230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 15768 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) : 2.248610 object centre at (A) : 32.84300 13.29950 20.78000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1014864 -1.117861 midg,1,midg; midg,igrid,midg -0.2801233 -0.2547541 1,midg,midg; igrid,midg,midg -0.2682805 4.2712584E-02 gauss-seidel spectral radius is 0.9993227 estimated iterations to convergence 303 setup time was (sec) 1.590000 now iterating at: 13:58:07 rms-change max change #iterations 11.13586 318.2750 at 10iterations 6.566538 125.0276 at 20iterations 3.873210 72.07136 at 30iterations 2.280332 39.25386 at 40iterations 1.340814 23.39069 at 50iterations 0.7904696 12.92743 at 60iterations 0.4658423 7.405990 at 70iterations 0.2732653 4.579105 at 80iterations 0.1610319 2.431834 at 90iterations 9.4688550E-02 1.477503 at 100iterations 5.5624727E-02 0.8383377 at 110iterations 3.2772582E-02 0.5099602 at 120iterations 1.9249732E-02 0.3050475 at 130iterations 1.1328803E-02 0.1720772 at 140iterations 6.6748220E-03 0.1039362 at 150iterations 3.9102151E-03 6.4167023E-02 at 160iterations 2.3078623E-03 3.7725925E-02 at 170iterations 1.3558873E-03 2.1138668E-02 at 180iterations finished qdiffx linear iterations at : 13:58:19 total time elapsed so far: 12.89000 # loops : 180 mean,max change (kT/e) : 1.3558873E-03 2.1138668E-02 energy calculations done at 12.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.03000 DelPhi exited at 13:58:19 13.029u 0.198s 0:13.74 96.1% 0+0k 0+0io 0pf+0w