Sat Oct 15 14:34:53 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 15 2011 at 14:34:53 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 = 2782 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: 0.6152145 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): -9.238000 48.62800 ymin,ymax (A): -8.106000 38.75900 zmin,zma (A): 1.683000 56.93200 x,y,z range (A): 57.86600 46.86500 55.24900 scale (grids/A): 0.6152145 object centre (A): 19.69500 15.32650 29.30750 number of atom coordinates read : 2782 total number of charged atoms : 2641 net assigned charge : -0.9999689 assigned positive charge : 418.0704 centred at (gu) : 89.02884 89.80910 88.28846 assigned negative charge : -419.0713 centred at (gu) : 88.93004 89.73499 88.27627 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7135 nv = 96 ne = 84 npr = 54996 no. pairs analyzed = 54996 no. exposed pairs = 3778 no. arc points = 26676 no. surface atoms = 1269 nbur = 1513 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 347 mr = 3619 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2000000 number of dielectric boundary points 3839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2701 ## 263 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8692 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9818063E-09 1.0000695E-10 midg,1,midg; midg,igrid,midg -5.4685052E-09 3.8011074E-09 1,midg,midg; igrid,midg,midg -8.4757543E-09 4.3947366E-09 gauss-seidel spectral radius is 0.9863447 estimated iterations to convergence 70 setup time was (sec) 0.4000000 now iterating at: 14:34:53 rms-change max change #iterations 0.1234906 20.27789 at 10iterations 1.1016682E-02 1.886345 at 20iterations 1.0105637E-03 0.1323814 at 30iterations 9.6874479E-05 1.4976501E-02 at 40iterations 1.1697067E-05 1.9531250E-03 at 50iterations finished qdiffx linear iterations at : 14:34:58 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 1.1697067E-05 1.9531250E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 14:34:59 3.538u 0.222s 0:05.97 62.8% 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 15 2011 at 14:34:59 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 = 2782 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: 1.845643 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): -9.238000 48.62800 ymin,ymax (A): -8.106000 38.75900 zmin,zma (A): 1.683000 56.93200 x,y,z range (A): 57.86600 46.86500 55.24900 scale (grids/A): 1.845643 object centre (A): 19.69500 15.32650 29.30750 number of atom coordinates read : 2782 total number of charged atoms : 2641 net assigned charge : -0.9999689 assigned positive charge : 418.0704 centred at (gu) : 87.08564 89.42673 84.86452 assigned negative charge : -419.0713 centred at (gu) : 86.78973 89.20479 84.82851 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77395 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26676 grid for indexing accessible points = 1.400000 m= 25874 mr = 51748 m= 3582 mr = 17853 m= 186 mr = 2021 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 447 time to turn everything in is 0.3800000 number of dielectric boundary points 35365 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 183 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20682 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) : 0.6152145 object centre at (A) : 19.69500 15.32650 29.30750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7399998E-03 1.5493990E-02 midg,1,midg; midg,igrid,midg -1.7717684E-02 7.1523045E-03 1,midg,midg; igrid,midg,midg -4.8411597E-02 2.4417875E-02 gauss-seidel spectral radius is 0.9985756 estimated iterations to convergence 210 setup time was (sec) 0.6300000 now iterating at: 14:35:00 rms-change max change #iterations 4.151563 187.9702 at 10iterations 1.904084 71.02091 at 20iterations 0.8709075 28.92564 at 30iterations 0.4009889 13.23901 at 40iterations 0.1839410 5.784447 at 50iterations 8.4559940E-02 3.047455 at 60iterations 3.8956083E-02 1.237267 at 70iterations 1.7882368E-02 0.5326385 at 80iterations 8.2266610E-03 0.2502937 at 90iterations 3.7874538E-03 0.1207228 at 100iterations 1.7506504E-03 5.5173159E-02 at 110iterations 8.0623309E-04 2.5647640E-02 at 120iterations finished qdiffx linear iterations at : 14:35:14 total time elapsed so far: 8.270000 # loops : 120 mean,max change (kT/e) : 8.0623309E-04 2.5647640E-02 energy calculations done at 8.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.400000 DelPhi exited at 14:35:14 8.407u 0.263s 0:15.32 56.5% 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 Sat Oct 15 2011 at 14:35:15 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 = 2782 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: 2.768465 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): -9.238000 48.62800 ymin,ymax (A): -8.106000 38.75900 zmin,zma (A): 1.683000 56.93200 x,y,z range (A): 57.86600 46.86500 55.24900 scale (grids/A): 2.768465 object centre (A): 19.69500 15.32650 29.30750 number of atom coordinates read : 2782 total number of charged atoms : 2641 net assigned charge : -0.9999689 assigned positive charge : 418.0704 centred at (gu) : 85.62830 89.13980 82.29672 assigned negative charge : -419.0713 centred at (gu) : 85.18461 88.80709 82.24268 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 179494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26676 grid for indexing accessible points = 1.400000 m= 85538 mr = 126637 m= 28376 mr = 67578 m= 6110 mr = 21651 m= 750 mr = 4255 m= 28 mr = 434 m= 0 mr = 7 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 1441 time to turn everything in is 1.050000 number of dielectric boundary points 79734 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 21127 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) : 1.845643 object centre at (A) : 19.69500 15.32650 29.30750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1525583 0.2924651 midg,1,midg; midg,igrid,midg -0.1376727 7.0816159E-02 1,midg,midg; igrid,midg,midg -0.6792865 0.2882049 gauss-seidel spectral radius is 0.9992639 estimated iterations to convergence 291 setup time was (sec) 1.360000 now iterating at: 14:35:16 rms-change max change #iterations 10.20354 387.9552 at 10iterations 6.089139 152.8215 at 20iterations 3.590760 82.68224 at 30iterations 2.100325 48.59420 at 40iterations 1.223104 23.54374 at 50iterations 0.7122982 15.33600 at 60iterations 0.4130982 9.378818 at 70iterations 0.2388187 5.140984 at 80iterations 0.1382325 2.580585 at 90iterations 7.9690516E-02 1.572750 at 100iterations 4.6069164E-02 0.7876606 at 110iterations 2.6571983E-02 0.5127144 at 120iterations 1.5288216E-02 0.2874832 at 130iterations 8.8111274E-03 0.1678181 at 140iterations 5.0733411E-03 8.9553833E-02 at 150iterations 2.9314633E-03 5.1769257E-02 at 160iterations 1.6897495E-03 3.0857086E-02 at 170iterations 9.7495277E-04 1.8224716E-02 at 180iterations finished qdiffx linear iterations at : 14:35:37 total time elapsed so far: 14.43000 # loops : 180 mean,max change (kT/e) : 9.7495277E-04 1.8224716E-02 energy calculations done at 14.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.56000 DelPhi exited at 14:35:38 14.559u 0.303s 0:23.68 62.7% 0+0k 0+0io 0pf+0w