Sun Oct 9 08:14:46 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 08:14:46 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3271 !!! WARNING: NDP 531 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5780159 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): 44.82000 106.4100 ymin,ymax (A): 20.46500 77.23300 zmin,zma (A): 10.69800 60.97700 x,y,z range (A): 61.59000 56.76800 50.27900 scale (grids/A): 0.5780159 object centre (A): 75.61501 48.84900 35.83750 number of atom coordinates read : 3271 total number of charged atoms : 3131 net assigned charge : 5.000012 assigned positive charge : 489.0839 centred at (gu) : 90.62552 90.68784 88.66794 assigned negative charge : -484.0850 centred at (gu) : 90.79128 90.64076 88.70351 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7159 nv = 96 ne = 84 npr = 66938 no. pairs analyzed = 66938 no. exposed pairs = 3919 no. arc points = 27612 no. surface atoms = 1313 nbur = 1958 mkacc time = 0.1100000 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 = 1.512000 m= 315 mr = 3916 m= 1 mr = 26 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 0.2400000 number of dielectric boundary points 3533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2793 ## 296 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9228 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4863311E-09 1.7701554E-10 midg,1,midg; midg,igrid,midg -2.1112317E-11 2.4370894E-09 1,midg,midg; igrid,midg,midg 4.0254498E-09 -3.2150371E-09 gauss-seidel spectral radius is 0.9845755 estimated iterations to convergence 66 setup time was (sec) 0.4400000 now iterating at: 08:14:47 rms-change max change #iterations 0.1063015 15.10519 at 10iterations 8.2747368E-03 1.419994 at 20iterations 6.5815449E-04 8.7833405E-02 at 30iterations 6.6321343E-05 1.0215759E-02 at 40iterations 1.0393691E-05 1.3070107E-03 at 50iterations finished qdiffx linear iterations at : 08:14:50 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.0393691E-05 1.3070107E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 08:14:51 3.414u 0.222s 0:04.31 84.2% 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 Sun Oct 9 2011 at 08:14:51 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3271 !!! WARNING: NDP 531 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.734048 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): 44.82000 106.4100 ymin,ymax (A): 20.46500 77.23300 zmin,zma (A): 10.69800 60.97700 x,y,z range (A): 61.59000 56.76800 50.27900 scale (grids/A): 1.734048 object centre (A): 75.61501 48.84900 35.83750 number of atom coordinates read : 3271 total number of charged atoms : 3131 net assigned charge : 5.000012 assigned positive charge : 489.0839 centred at (gu) : 91.87572 92.06230 86.00278 assigned negative charge : -484.0850 centred at (gu) : 92.37341 91.92180 86.11017 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 78861 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27612 grid for indexing accessible points = 1.400000 m= 26723 mr = 55081 m= 3171 mr = 19182 m= 114 mr = 1713 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 756 time to turn everything in is 0.4000000 number of dielectric boundary points 32875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 237 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 24321 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) : 0.5780159 object centre at (A) : 75.61501 48.84900 35.83750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2951208E-03 -1.9781545E-03 midg,1,midg; midg,igrid,midg -9.9184560E-03 4.5965794E-03 1,midg,midg; igrid,midg,midg 4.4477582E-02 -1.5019728E-02 gauss-seidel spectral radius is 0.9984271 estimated iterations to convergence 200 setup time was (sec) 0.6200000 now iterating at: 08:14:52 rms-change max change #iterations 3.991066 154.5988 at 10iterations 1.762618 60.21045 at 20iterations 0.7809311 25.23065 at 30iterations 0.3462377 10.88885 at 40iterations 0.1531693 4.706026 at 50iterations 6.8093106E-02 2.422812 at 60iterations 3.0180324E-02 0.9288180 at 70iterations 1.3464097E-02 0.4181566 at 80iterations 5.9460322E-03 0.1909237 at 90iterations 2.6341507E-03 8.6963654E-02 at 100iterations 1.1741857E-03 3.9510727E-02 at 110iterations 5.2043685E-04 1.6620636E-02 at 120iterations finished qdiffx linear iterations at : 08:14:59 total time elapsed so far: 8.410000 # loops : 120 mean,max change (kT/e) : 5.2043685E-04 1.6620636E-02 energy calculations done at 8.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.540000 DelPhi exited at 08:15:00 8.541u 0.242s 0:09.17 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 08:15:00 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3271 !!! WARNING: NDP 531 has a net charge of -3.0000 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: 2.601071 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): 44.82000 106.4100 ymin,ymax (A): 20.46500 77.23300 zmin,zma (A): 10.69800 60.97700 x,y,z range (A): 61.59000 56.76800 50.27900 scale (grids/A): 2.601071 object centre (A): 75.61501 48.84900 35.83750 number of atom coordinates read : 3271 total number of charged atoms : 3131 net assigned charge : 5.000012 assigned positive charge : 489.0839 centred at (gu) : 92.81353 93.09324 84.00409 assigned negative charge : -484.0850 centred at (gu) : 93.55983 92.88256 84.16515 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 183352 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27612 grid for indexing accessible points = 1.400000 m= 88935 mr = 134417 m= 28967 mr = 71901 m= 5323 mr = 22770 m= 514 mr = 3637 m= 7 mr = 282 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 2385 time to turn everything in is 0.9600000 number of dielectric boundary points 74091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 25036 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) : 1.734048 object centre at (A) : 75.61501 48.84900 35.83750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9569357E-02 -3.5446480E-02 midg,1,midg; midg,igrid,midg -0.1925323 5.0051179E-02 1,midg,midg; igrid,midg,midg 0.4964587 -0.1989525 gauss-seidel spectral radius is 0.9992152 estimated iterations to convergence 282 setup time was (sec) 1.190000 now iterating at: 08:15:01 rms-change max change #iterations 9.920230 313.3049 at 10iterations 5.752055 136.5094 at 20iterations 3.311273 73.76975 at 30iterations 1.895814 42.93822 at 40iterations 1.084900 22.59307 at 50iterations 0.6183676 12.00880 at 60iterations 0.3516256 7.662167 at 70iterations 0.1998260 4.208630 at 80iterations 0.1134792 2.427577 at 90iterations 6.4386994E-02 1.311428 at 100iterations 3.6446877E-02 0.6348441 at 110iterations 2.0647800E-02 0.4129677 at 120iterations 1.1701043E-02 0.2080812 at 130iterations 6.6259839E-03 0.1324348 at 140iterations 3.7424366E-03 6.9506645E-02 at 150iterations 2.1195326E-03 3.9398193E-02 at 160iterations 1.2004136E-03 2.2142410E-02 at 170iterations 6.7773904E-04 1.2317657E-02 at 180iterations finished qdiffx linear iterations at : 08:15:13 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 6.7773904E-04 1.2317657E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.64000 DelPhi exited at 08:15:13 12.644u 0.236s 0:13.64 94.3% 0+0k 0+0io 0pf+0w