Mon Oct 10 14:00:21 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 14:00:21 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1343 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7462217 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): -21.62700 21.08400 ymin,ymax (A): -61.17300 -13.46600 zmin,zma (A): 7.414000 45.50500 x,y,z range (A): 42.71100 47.70700 38.09100 scale (grids/A): 0.7462217 object centre (A): -0.2715006 -37.31950 26.45950 number of atom coordinates read : 1343 total number of charged atoms : 1273 net assigned charge : -0.4999965 assigned positive charge : 205.7722 centred at (gu) : 90.88941 91.13029 89.79560 assigned negative charge : -206.2722 centred at (gu) : 90.69785 91.00703 89.74023 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5320 nv = 96 ne = 84 npr = 26137 no. pairs analyzed = 26137 no. exposed pairs = 1775 no. arc points = 12912 no. surface atoms = 611 nbur = 732 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 387 mr = 2826 m= 4 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1200000 number of dielectric boundary points 2808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 942 ## 55 charges are in solution ## iepsmp to db, and charging done at 0.1900000 number of grid points assigned charge 5515 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5711258E-08 2.7431128E-08 midg,1,midg; midg,igrid,midg -8.4724412E-08 9.7108966E-08 1,midg,midg; igrid,midg,midg -1.3272577E-07 1.5095311E-07 gauss-seidel spectral radius is 0.9905685 estimated iterations to convergence 84 setup time was (sec) 0.3000000 now iterating at: 14:00:22 rms-change max change #iterations 0.2077014 35.99497 at 10iterations 2.8424989E-02 4.605677 at 20iterations 3.8267220E-03 0.6573849 at 30iterations 5.1428773E-04 8.9715004E-02 at 40iterations 7.0225178E-05 1.3973236E-02 at 50iterations finished qdiffx linear iterations at : 14:00:25 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 7.0225178E-05 1.3973236E-02 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 14:00:25 3.247u 0.173s 0:04.02 84.8% 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 Mon Oct 10 2011 at 14:00:25 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1343 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.238665 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): -21.62700 21.08400 ymin,ymax (A): -61.17300 -13.46600 zmin,zma (A): 7.414000 45.50500 x,y,z range (A): 42.71100 47.70700 38.09100 scale (grids/A): 2.238665 object centre (A): -0.2715006 -37.31950 26.45950 number of atom coordinates read : 1343 total number of charged atoms : 1273 net assigned charge : -0.4999965 assigned positive charge : 205.7722 centred at (gu) : 92.66851 93.39095 89.38703 assigned negative charge : -206.2722 centred at (gu) : 92.09369 93.02137 89.22093 start vw surface at 5.0000001E-02 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 56248 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12912 grid for indexing accessible points = 1.400000 m= 21591 mr = 37837 m= 4993 mr = 16119 m= 624 mr = 3377 m= 30 mr = 352 m= 0 mr = 5 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 25796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 10144 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) : 0.7462217 object centre at (A) : -0.2715006 -37.31950 26.45950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4903829E-03 8.6211422E-03 midg,1,midg; midg,igrid,midg -2.4572842E-02 1.4371521E-02 1,midg,midg; igrid,midg,midg -3.2730300E-02 1.8185508E-03 gauss-seidel spectral radius is 0.9988744 estimated iterations to convergence 236 setup time was (sec) 0.4800000 now iterating at: 14:00:26 rms-change max change #iterations 4.104582 216.4556 at 10iterations 2.063821 82.50346 at 20iterations 1.039231 37.92857 at 30iterations 0.5184727 19.99545 at 40iterations 0.2611711 8.645506 at 50iterations 0.1308838 4.918592 at 60iterations 6.5495856E-02 2.111907 at 70iterations 3.2974418E-02 1.191463 at 80iterations 1.6514175E-02 0.5548096 at 90iterations 8.2763741E-03 0.2709410 at 100iterations 4.1546747E-03 0.1440411 at 110iterations 2.0894408E-03 7.0636272E-02 at 120iterations finished qdiffx linear iterations at : 14:00:33 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 2.0894408E-03 7.0636272E-02 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.480000 DelPhi exited at 14:00:34 7.485u 0.215s 0:08.57 89.7% 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 Mon Oct 10 2011 at 14:00:34 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1343 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.357998 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): -21.62700 21.08400 ymin,ymax (A): -61.17300 -13.46600 zmin,zma (A): 7.414000 45.50500 x,y,z range (A): 42.71100 47.70700 38.09100 scale (grids/A): 3.357998 object centre (A): -0.2715006 -37.31950 26.45950 number of atom coordinates read : 1343 total number of charged atoms : 1273 net assigned charge : -0.4999965 assigned positive charge : 205.7722 centred at (gu) : 94.00285 95.08649 89.08067 assigned negative charge : -206.2722 centred at (gu) : 93.14067 94.53215 88.83147 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 129483 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12912 grid for indexing accessible points = 1.400000 m= 66517 mr = 91393 m= 28391 mr = 54578 m= 9681 mr = 23158 m= 2456 mr = 7535 m= 391 mr = 1790 m= 29 mr = 278 m= 0 mr = 17 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 number of dielectric boundary points 58199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 10184 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) : 2.238665 object centre at (A) : -0.2715006 -37.31950 26.45950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1841925 4.2685121E-02 midg,1,midg; midg,igrid,midg -0.1896282 2.1296203E-02 1,midg,midg; igrid,midg,midg -0.3050844 -1.2675798E-02 gauss-seidel spectral radius is 0.9993024 estimated iterations to convergence 299 setup time was (sec) 1.090000 now iterating at: 14:00:35 rms-change max change #iterations 8.908608 302.4573 at 10iterations 5.187851 136.0042 at 20iterations 3.040612 66.60655 at 30iterations 1.765858 35.82458 at 40iterations 1.032465 20.59800 at 50iterations 0.6020880 12.08968 at 60iterations 0.3507299 6.506504 at 70iterations 0.2045214 3.860052 at 80iterations 0.1190692 2.533376 at 90iterations 6.9406435E-02 1.409180 at 100iterations 4.0482804E-02 0.7431030 at 110iterations 2.3604894E-02 0.4629402 at 120iterations 1.3767832E-02 0.2668915 at 130iterations 7.9968031E-03 0.1555262 at 140iterations 4.6780300E-03 9.7595215E-02 at 150iterations 2.7180659E-03 5.1891327E-02 at 160iterations 1.5883826E-03 3.1575680E-02 at 170iterations 9.2184771E-04 1.7576218E-02 at 180iterations finished qdiffx linear iterations at : 14:00:46 total time elapsed so far: 11.88000 # loops : 180 mean,max change (kT/e) : 9.2184771E-04 1.7576218E-02 energy calculations done at 11.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.00000 DelPhi exited at 14:00:47 12.006u 0.203s 0:12.67 96.2% 0+0k 0+0io 0pf+0w