Sat Oct 8 14:16:58 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 Sat Oct 8 2011 at 14:16:58 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3001 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6320238 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): -35.49200 11.42800 ymin,ymax (A): -15.12700 36.11100 zmin,zma (A): -45.35200 10.97500 x,y,z range (A): 46.92000 51.23800 56.32700 scale (grids/A): 0.6320238 object centre (A): -12.03200 10.49200 -17.18850 number of atom coordinates read : 3001 total number of charged atoms : 2854 net assigned charge : -0.9999939 assigned positive charge : 449.6886 centred at (gu) : 89.01428 88.99236 87.60837 assigned negative charge : -450.6894 centred at (gu) : 88.99476 88.91901 87.71170 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7873 nv = 96 ne = 84 npr = 63097 no. pairs analyzed = 63097 no. exposed pairs = 3475 no. arc points = 23892 no. surface atoms = 1176 nbur = 1825 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 4605 m= 6 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3624 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2338 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9698 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6610759E-08 -7.4998496E-09 midg,1,midg; midg,igrid,midg -1.1608165E-08 5.2177249E-09 1,midg,midg; igrid,midg,midg -4.2539559E-09 6.1598315E-10 gauss-seidel spectral radius is 0.9870591 estimated iterations to convergence 72 setup time was (sec) 0.6700000 now iterating at: 14:16:59 rms-change max change #iterations 0.1519021 22.58505 at 10iterations 1.4908055E-02 2.008358 at 20iterations 1.5655109E-03 0.2056923 at 30iterations 1.9015314E-04 2.4589539E-02 at 40iterations 3.0794483E-05 4.2018890E-03 at 50iterations finished qdiffx linear iterations at : 14:17:02 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 3.0794483E-05 4.2018890E-03 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 14:17:03 4.198u 0.269s 0:04.95 89.8% 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 Sat Oct 8 2011 at 14:17:03 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3001 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.896071 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): -35.49200 11.42800 ymin,ymax (A): -15.12700 36.11100 zmin,zma (A): -45.35200 10.97500 x,y,z range (A): 46.92000 51.23800 56.32700 scale (grids/A): 1.896071 object centre (A): -12.03200 10.49200 -17.18850 number of atom coordinates read : 3001 total number of charged atoms : 2854 net assigned charge : -0.9999939 assigned positive charge : 449.6886 centred at (gu) : 87.04241 86.97653 82.82449 assigned negative charge : -450.6894 centred at (gu) : 86.98406 86.75671 83.13500 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 86412 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23892 grid for indexing accessible points = 1.400000 m= 31044 mr = 62560 m= 4416 mr = 23284 m= 202 mr = 2663 m= 0 mr = 62 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7500000 number of dielectric boundary points 33505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 22407 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) : 0.6320238 object centre at (A) : -12.03200 10.49200 -17.18850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7264276E-02 -2.8885193E-02 midg,1,midg; midg,igrid,midg -4.3327282E-03 1.9291993E-02 1,midg,midg; igrid,midg,midg -9.3230549E-03 -8.2513802E-03 gauss-seidel spectral radius is 0.9986522 estimated iterations to convergence 216 setup time was (sec) 1.050000 now iterating at: 14:17:04 rms-change max change #iterations 4.599752 183.1625 at 10iterations 2.165431 71.72775 at 20iterations 1.023587 35.93287 at 30iterations 0.4811919 13.51995 at 40iterations 0.2270668 6.418178 at 50iterations 0.1072667 3.052456 at 60iterations 5.0688341E-02 1.512705 at 70iterations 2.3820544E-02 0.6896667 at 80iterations 1.1241450E-02 0.3445902 at 90iterations 5.3087929E-03 0.1750565 at 100iterations 2.5098999E-03 8.5010529E-02 at 110iterations 1.1855767E-03 3.9258003E-02 at 120iterations finished qdiffx linear iterations at : 14:17:13 total time elapsed so far: 9.610000 # loops : 120 mean,max change (kT/e) : 1.1855767E-03 3.9258003E-02 energy calculations done at 9.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.790000 DelPhi exited at 14:17:13 9.794u 0.323s 0:10.40 97.2% 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 Sat Oct 8 2011 at 14:17:13 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3001 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.844107 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): -35.49200 11.42800 ymin,ymax (A): -15.12700 36.11100 zmin,zma (A): -45.35200 10.97500 x,y,z range (A): 46.92000 51.23800 56.32700 scale (grids/A): 2.844107 object centre (A): -12.03200 10.49200 -17.18850 number of atom coordinates read : 3001 total number of charged atoms : 2854 net assigned charge : -0.9999939 assigned positive charge : 449.6886 centred at (gu) : 85.56341 85.46465 79.23676 assigned negative charge : -450.6894 centred at (gu) : 85.47597 85.13503 79.70239 start vw surface at 0.1700000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 200205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23892 grid for indexing accessible points = 1.400000 m= 102308 mr = 151076 m= 35362 mr = 85173 m= 7553 mr = 28567 m= 891 mr = 5522 m= 43 mr = 556 m= 0 mr = 9 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.940000 number of dielectric boundary points 75459 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 22831 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) : 1.896071 object centre at (A) : -12.03200 10.49200 -17.18850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7244600 -0.2836437 midg,1,midg; midg,igrid,midg 6.2263019E-02 0.2425650 1,midg,midg; igrid,midg,midg -5.7082236E-02 -5.2750796E-02 gauss-seidel spectral radius is 0.9992653 estimated iterations to convergence 291 setup time was (sec) 2.290000 now iterating at: 14:17:16 rms-change max change #iterations 10.72208 328.4834 at 10iterations 6.287652 172.4897 at 20iterations 3.655480 78.37648 at 30iterations 2.123919 40.84263 at 40iterations 1.235727 27.79684 at 50iterations 0.7144439 13.01730 at 60iterations 0.4130486 8.455917 at 70iterations 0.2385376 3.859573 at 80iterations 0.1377877 2.348869 at 90iterations 7.9609238E-02 1.349000 at 100iterations 4.6060909E-02 0.8179293 at 110iterations 2.6587073E-02 0.4575405 at 120iterations 1.5353342E-02 0.2681885 at 130iterations 8.8696042E-03 0.1508284 at 140iterations 5.1217633E-03 8.7901115E-02 at 150iterations 2.9642049E-03 5.0357819E-02 at 160iterations 1.7231206E-03 2.7870178E-02 at 170iterations 1.0045322E-03 1.6769409E-02 at 180iterations finished qdiffx linear iterations at : 14:17:30 total time elapsed so far: 16.55000 # loops : 180 mean,max change (kT/e) : 1.0045322E-03 1.6769409E-02 energy calculations done at 16.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.74000 DelPhi exited at 14:17:31 16.742u 0.319s 0:17.38 98.1% 0+0k 0+0io 0pf+0w