Mon Oct 10 13:58:20 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 Mon Oct 10 2011 at 13:58:20 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: 253 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 : 317.0319 centred at (gu) : 89.16469 90.80050 89.76164 assigned negative charge : -323.0320 centred at (gu) : 89.19527 90.86066 89.93021 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-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 = 6.9999993E-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 = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 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 0.2500000 number of grid points assigned charge 8548 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.0263874E-08 -3.2742923E-07 midg,1,midg; midg,igrid,midg -4.8620453E-08 -2.3702653E-07 1,midg,midg; igrid,midg,midg -1.0606916E-07 -1.4427506E-07 gauss-seidel spectral radius is 0.9907237 estimated iterations to convergence 84 setup time was (sec) 0.3700000 now iterating at: 13:58:20 rms-change max change #iterations 0.2621984 35.43648 at 10iterations 3.5826579E-02 4.218540 at 20iterations 4.9351947E-03 0.5978775 at 30iterations 7.0221088E-04 8.1288338E-02 at 40iterations 9.5368880E-05 1.4438629E-02 at 50iterations finished qdiffx linear iterations at : 13:58:23 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 9.5368880E-05 1.4438629E-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) 3.310000 DelPhi exited at 13:58:24 3.316u 0.160s 0:03.96 87.6% 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 13:58:24 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: 253 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 : 317.0319 centred at (gu) : 87.49416 92.40140 89.28468 assigned negative charge : -323.0320 centred at (gu) : 87.58581 92.58198 89.79063 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 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 0.4300000 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 0.5000000 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 5.7084216E-03 -0.1272114 midg,1,midg; midg,igrid,midg -3.6091667E-02 -4.6642847E-02 1,midg,midg; igrid,midg,midg -9.1279577E-03 3.0725664E-03 gauss-seidel spectral radius is 0.9989479 estimated iterations to convergence 244 setup time was (sec) 0.6300000 now iterating at: 13:58:24 rms-change max change #iterations 5.253911 213.7820 at 10iterations 2.673677 81.28740 at 20iterations 1.375868 43.49774 at 30iterations 0.7058011 19.35697 at 40iterations 0.3619368 11.84549 at 50iterations 0.1859739 5.199595 at 60iterations 9.5492817E-02 2.501366 at 70iterations 4.9067426E-02 1.413382 at 80iterations 2.5166523E-02 0.6595001 at 90iterations 1.2944494E-02 0.3738976 at 100iterations 6.6292705E-03 0.1797981 at 110iterations 3.4084483E-03 9.7428799E-02 at 120iterations finished qdiffx linear iterations at : 13:58:31 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 3.4084483E-03 9.7428799E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 13:58:32 7.775u 0.204s 0:08.29 96.1% 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 Mon Oct 10 2011 at 13:58:32 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: 253 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 : 317.0319 centred at (gu) : 86.24120 93.60201 88.92700 assigned negative charge : -323.0320 centred at (gu) : 86.37870 93.87292 89.68590 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5500000 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 1.430000 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 0.1011002 -1.128653 midg,1,midg; midg,igrid,midg -0.2993178 -0.2494257 1,midg,midg; igrid,midg,midg -0.2592715 5.4108530E-02 gauss-seidel spectral radius is 0.9993227 estimated iterations to convergence 303 setup time was (sec) 1.570000 now iterating at: 13:58:34 rms-change max change #iterations 11.19536 318.2749 at 10iterations 6.603265 125.0276 at 20iterations 3.894286 72.06966 at 30iterations 2.292975 39.47694 at 40iterations 1.347968 23.19612 at 50iterations 0.7947279 13.04742 at 60iterations 0.4683135 7.506737 at 70iterations 0.2747360 4.693508 at 80iterations 0.1619103 2.462216 at 90iterations 9.5180079E-02 1.465834 at 100iterations 5.5912659E-02 0.8476830 at 110iterations 3.2942135E-02 0.5235329 at 120iterations 1.9354573E-02 0.3080301 at 130iterations 1.1388495E-02 0.1742265 at 140iterations 6.7090145E-03 0.1044647 at 150iterations 3.9304136E-03 6.4903259E-02 at 160iterations 2.3199527E-03 3.8105011E-02 at 170iterations 1.3630252E-03 2.1102905E-02 at 180iterations finished qdiffx linear iterations at : 13:58:45 total time elapsed so far: 12.87000 # loops : 180 mean,max change (kT/e) : 1.3630252E-03 2.1102905E-02 energy calculations done at 12.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 13:58:46 13.006u 0.205s 0:13.60 97.0% 0+0k 0+0io 0pf+0w