Sun Oct 9 13:12:52 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 Sun Oct 9 2011 at 13:12:52 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 = 2399 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: 0.6680678 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): -6.862000 44.10100 ymin,ymax (A): 22.84700 76.13500 zmin,zma (A): 42.15400 85.05400 x,y,z range (A): 50.96300 53.28800 42.90000 scale (grids/A): 0.6680678 object centre (A): 18.61950 49.49100 63.60400 number of atom coordinates read : 2399 total number of charged atoms : 2257 net assigned charge : 2.500025 assigned positive charge : 364.7420 centred at (gu) : 89.71252 90.50838 90.55548 assigned negative charge : -362.2425 centred at (gu) : 89.75512 90.71657 90.60843 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7142 nv = 96 ne = 84 npr = 48327 no. pairs analyzed = 48327 no. exposed pairs = 2900 no. arc points = 20532 no. surface atoms = 979 nbur = 1420 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 458 mr = 3961 m= 3 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.1900000 number of dielectric boundary points 3558 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2024 ## 194 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8394 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8008151E-08 -4.3312998E-09 midg,1,midg; midg,igrid,midg 4.8933124E-08 -4.4507917E-08 1,midg,midg; igrid,midg,midg 1.8944162E-08 -1.3243123E-09 gauss-seidel spectral radius is 0.9883667 estimated iterations to convergence 76 setup time was (sec) 0.3800000 now iterating at: 13:12:52 rms-change max change #iterations 0.1681253 23.68509 at 10iterations 1.8299775E-02 2.371887 at 20iterations 2.1065173E-03 0.3108196 at 30iterations 2.7184372E-04 3.5179138E-02 at 40iterations 5.1179257E-05 7.4558258E-03 at 50iterations finished qdiffx linear iterations at : 13:12:55 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 5.1179257E-05 7.4558258E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 13:12:56 3.426u 0.166s 0:03.87 92.5% 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 Sun Oct 9 2011 at 13:12:56 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 = 2399 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.004204 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): -6.862000 44.10100 ymin,ymax (A): 22.84700 76.13500 zmin,zma (A): 42.15400 85.05400 x,y,z range (A): 50.96300 53.28800 42.90000 scale (grids/A): 2.004204 object centre (A): 18.61950 49.49100 63.60400 number of atom coordinates read : 2399 total number of charged atoms : 2257 net assigned charge : 2.500025 assigned positive charge : 364.7420 centred at (gu) : 89.13716 91.52462 91.66599 assigned negative charge : -362.2425 centred at (gu) : 89.26523 92.14950 91.82500 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 76717 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20532 grid for indexing accessible points = 1.400000 m= 28667 mr = 53416 m= 4971 mr = 21269 m= 427 mr = 3169 m= 5 mr = 225 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 868 time to turn everything in is 0.3900000 number of dielectric boundary points 32708 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 17851 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) : 0.6680678 object centre at (A) : 18.61950 49.49100 63.60400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2840792E-02 3.8216372E-03 midg,1,midg; midg,igrid,midg 2.5779616E-02 -5.6393459E-02 1,midg,midg; igrid,midg,midg 4.2076174E-02 -9.4995303E-03 gauss-seidel spectral radius is 0.9987462 estimated iterations to convergence 224 setup time was (sec) 0.6100000 now iterating at: 13:12:57 rms-change max change #iterations 4.477189 210.4453 at 10iterations 2.160523 73.77762 at 20iterations 1.044722 33.71561 at 30iterations 0.5050370 16.26510 at 40iterations 0.2448374 7.617950 at 50iterations 0.1181260 3.673077 at 60iterations 5.7076849E-02 1.779470 at 70iterations 2.7607542E-02 0.7920389 at 80iterations 1.3373258E-02 0.3997338 at 90iterations 6.5030735E-03 0.1990776 at 100iterations 3.1636443E-03 9.5043182E-02 at 110iterations 1.5416846E-03 4.6676636E-02 at 120iterations finished qdiffx linear iterations at : 13:13:04 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 1.5416846E-03 4.6676636E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 13:13:04 7.864u 0.199s 0:08.40 95.8% 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 13:13:04 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 = 2399 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.006305 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): -6.862000 44.10100 ymin,ymax (A): 22.84700 76.13500 zmin,zma (A): 42.15400 85.05400 x,y,z range (A): 50.96300 53.28800 42.90000 scale (grids/A): 3.006305 object centre (A): 18.61950 49.49100 63.60400 number of atom coordinates read : 2399 total number of charged atoms : 2257 net assigned charge : 2.500025 assigned positive charge : 364.7420 centred at (gu) : 88.70567 92.28693 92.49887 assigned negative charge : -362.2425 centred at (gu) : 88.89775 93.22427 92.73739 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 177009 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20532 grid for indexing accessible points = 1.400000 m= 91769 mr = 129054 m= 34552 mr = 75360 m= 9200 mr = 28036 m= 1787 mr = 6943 m= 161 mr = 1334 m= 1 mr = 102 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 2804 time to turn everything in is 1.000000 number of dielectric boundary points 73650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 18052 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) : 2.004204 object centre at (A) : 18.61950 49.49100 63.60400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3627142 -2.0312026E-02 midg,1,midg; midg,igrid,midg 0.4963175 -0.6072804 1,midg,midg; igrid,midg,midg 0.4321745 -0.2644055 gauss-seidel spectral radius is 0.9992777 estimated iterations to convergence 294 setup time was (sec) 1.240000 now iterating at: 13:13:06 rms-change max change #iterations 10.27683 451.3627 at 10iterations 6.023247 136.9593 at 20iterations 3.535627 68.51471 at 30iterations 2.069401 41.95147 at 40iterations 1.205104 24.85428 at 50iterations 0.7016951 13.35928 at 60iterations 0.4089391 7.904955 at 70iterations 0.2370917 4.487778 at 80iterations 0.1377679 2.381864 at 90iterations 7.9984754E-02 1.397340 at 100iterations 4.6379156E-02 0.9611340 at 110iterations 2.6976705E-02 0.5448341 at 120iterations 1.5638307E-02 0.2661067 at 130iterations 9.0942504E-03 0.1555443 at 140iterations 5.2899602E-03 9.4099998E-02 at 150iterations 3.0903465E-03 6.4659119E-02 at 160iterations 1.8140582E-03 3.4812927E-02 at 170iterations 1.0757850E-03 2.1806717E-02 at 180iterations finished qdiffx linear iterations at : 13:13:17 total time elapsed so far: 12.57000 # loops : 180 mean,max change (kT/e) : 1.0757850E-03 2.1806717E-02 energy calculations done at 12.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 13:13:17 12.700u 0.213s 0:13.24 97.5% 0+0k 0+0io 0pf+0w