Sun Oct 9 10:48:44 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 10:48:44 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 = 3034 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: 0.5814713 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): -60.80100 0.4230000 ymin,ymax (A): -25.78200 32.00800 zmin,zma (A): -3.686000 53.50500 x,y,z range (A): 61.22400 57.79000 57.19100 scale (grids/A): 0.5814713 object centre (A): -30.18900 3.113000 24.90950 number of atom coordinates read : 3034 total number of charged atoms : 2891 net assigned charge : 5.500008 assigned positive charge : 443.7849 centred at (gu) : 89.69943 88.57819 92.03125 assigned negative charge : -438.2867 centred at (gu) : 89.68977 88.53223 92.01669 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6954 nv = 96 ne = 84 npr = 60268 no. pairs analyzed = 60268 no. exposed pairs = 4129 no. arc points = 29526 no. surface atoms = 1373 nbur = 1661 mkacc time = 0.1000000 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 = 1.484000 m= 323 mr = 3497 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3760 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2968 ## 320 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8817 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9897642E-10 2.5508411E-09 midg,1,midg; midg,igrid,midg 2.8003369E-10 1.6592540E-09 1,midg,midg; igrid,midg,midg 1.1194624E-09 1.3857949E-09 gauss-seidel spectral radius is 0.9847515 estimated iterations to convergence 66 setup time was (sec) 0.3900000 now iterating at: 10:48:44 rms-change max change #iterations 9.9435627E-02 17.79435 at 10iterations 7.7746646E-03 1.094795 at 20iterations 7.7710167E-04 0.1249418 at 30iterations 1.3745870E-04 2.2551231E-02 at 40iterations 3.6017977E-05 5.8917999E-03 at 50iterations finished qdiffx linear iterations at : 10:48:47 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 3.6017977E-05 5.8917999E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 10:48:48 3.351u 0.184s 0:03.84 91.9% 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 10:48:48 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 = 3034 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: 1.744414 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): -60.80100 0.4230000 ymin,ymax (A): -25.78200 32.00800 zmin,zma (A): -3.686000 53.50500 x,y,z range (A): 61.22400 57.79000 57.19100 scale (grids/A): 1.744414 object centre (A): -30.18900 3.113000 24.90950 number of atom coordinates read : 3034 total number of charged atoms : 2891 net assigned charge : 5.500008 assigned positive charge : 443.7849 centred at (gu) : 89.09731 85.73349 96.09275 assigned negative charge : -438.2867 centred at (gu) : 89.06911 85.59656 96.05003 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 76467 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29526 grid for indexing accessible points = 1.400000 m= 24252 mr = 50945 m= 3362 mr = 16471 m= 164 mr = 1790 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 35010 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 207 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 22484 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) : 0.5814713 object centre at (A) : -30.18900 3.113000 24.90950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0550569E-03 1.2371144E-02 midg,1,midg; midg,igrid,midg 2.0678345E-02 1.4363896E-02 1,midg,midg; igrid,midg,midg 1.0040560E-02 -7.0684538E-03 gauss-seidel spectral radius is 0.9984429 estimated iterations to convergence 201 setup time was (sec) 0.5600000 now iterating at: 10:48:49 rms-change max change #iterations 3.803512 183.1558 at 10iterations 1.673255 59.41733 at 20iterations 0.7434360 26.39582 at 30iterations 0.3299007 11.14786 at 40iterations 0.1471549 5.016266 at 50iterations 6.5352313E-02 2.059508 at 60iterations 2.9165016E-02 0.8889065 at 70iterations 1.2933003E-02 0.4727764 at 80iterations 5.7837404E-03 0.1891956 at 90iterations 2.6021714E-03 8.7633133E-02 at 100iterations 1.1756568E-03 3.6294937E-02 at 110iterations 5.3924788E-04 1.7360687E-02 at 120iterations finished qdiffx linear iterations at : 10:48:55 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 5.3924788E-04 1.7360687E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 10:48:56 7.676u 0.210s 0:08.23 95.7% 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 Sun Oct 9 2011 at 10:48:56 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 = 3034 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: 2.616621 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): -60.80100 0.4230000 ymin,ymax (A): -25.78200 32.00800 zmin,zma (A): -3.686000 53.50500 x,y,z range (A): 61.22400 57.79000 57.19100 scale (grids/A): 2.616621 object centre (A): -30.18900 3.113000 24.90950 number of atom coordinates read : 3034 total number of charged atoms : 2891 net assigned charge : 5.500008 assigned positive charge : 443.7849 centred at (gu) : 88.64561 83.59988 99.13898 assigned negative charge : -438.2867 centred at (gu) : 88.60371 83.39478 99.07513 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 177810 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29526 grid for indexing accessible points = 1.400000 m= 81282 mr = 125178 m= 26120 mr = 63293 m= 5392 mr = 19752 m= 577 mr = 3607 m= 20 mr = 323 m= 0 mr = 4 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9100000 number of dielectric boundary points 79044 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 23119 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) : 1.744414 object centre at (A) : -30.18900 3.113000 24.90950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1735374E-02 0.2135004 midg,1,midg; midg,igrid,midg 0.4405584 0.1888961 1,midg,midg; igrid,midg,midg 0.1871415 -0.2056172 gauss-seidel spectral radius is 0.9992218 estimated iterations to convergence 283 setup time was (sec) 1.150000 now iterating at: 10:48:57 rms-change max change #iterations 9.527844 300.8749 at 10iterations 5.582555 163.1380 at 20iterations 3.232031 69.39924 at 30iterations 1.865660 41.89633 at 40iterations 1.072053 22.81318 at 50iterations 0.6145127 12.14865 at 60iterations 0.3507297 7.392143 at 70iterations 0.1997955 4.400585 at 80iterations 0.1136893 2.251339 at 90iterations 6.4765334E-02 1.181236 at 100iterations 3.6800798E-02 0.7059665 at 110iterations 2.0935373E-02 0.3783798 at 120iterations 1.1885435E-02 0.2101898 at 130iterations 6.7664171E-03 0.1268768 at 140iterations 3.8520128E-03 6.8466187E-02 at 150iterations 2.2021919E-03 4.2017937E-02 at 160iterations 1.2663193E-03 2.3958206E-02 at 170iterations 7.3595496E-04 1.4335632E-02 at 180iterations finished qdiffx linear iterations at : 10:49:09 total time elapsed so far: 12.33000 # loops : 180 mean,max change (kT/e) : 7.3595496E-04 1.4335632E-02 energy calculations done at 12.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 10:49:09 12.465u 0.212s 0:13.10 96.7% 0+0k 0+0io 0pf+0w