Wed Dec 21 14:21:51 PST 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 Wed Dec 21 2011 at 14:21:55 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1906 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 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: 0.6111693 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): -23.64600 34.60300 ymin,ymax (A): -19.12200 20.44400 zmin,zma (A): -3.341000 39.07900 x,y,z range (A): 58.24900 39.56600 42.42000 scale (grids/A): 0.6111693 object centre (A): 5.478500 0.6610003 17.86900 number of atom coordinates read : 1906 total number of charged atoms : 1774 net assigned charge : 8.0009013E-02 assigned positive charge : 282.5200 centred at (gu) : 89.79189 90.33685 90.30300 assigned negative charge : -282.4403 centred at (gu) : 89.79478 90.39415 90.39865 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4803 nv = 96 ne = 84 npr = 39375 no. pairs analyzed = 39375 no. exposed pairs = 2501 no. arc points = 17404 no. surface atoms = 853 nbur = 1053 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 238 mr = 2556 m= 2 mr = 14 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 0.2900000 number of dielectric boundary points 2473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1782 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 5840 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3628400E-09 -3.7901717E-09 midg,1,midg; midg,igrid,midg 2.0344473E-09 -2.2472733E-09 1,midg,midg; igrid,midg,midg 1.8812461E-10 -3.4975967E-11 gauss-seidel spectral radius is 0.9860811 estimated iterations to convergence 69 setup time was (sec) 0.6000000 now iterating at: 14:21:57 rms-change max change #iterations 0.1007886 19.25854 at 10iterations 9.0679526E-03 1.694160 at 20iterations 7.7609532E-04 0.1326885 at 30iterations 7.0374736E-05 1.2243271E-02 at 40iterations 6.2428021E-06 1.0685921E-03 at 50iterations finished qdiffx linear iterations at : 14:22:01 total time elapsed so far: 4.910000 # loops : 50 mean,max change (kT/e) : 6.2428021E-06 1.0685921E-03 energy calculations done at 4.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.100000 DelPhi exited at 14:22:06 5.107u 0.404s 0:12.38 44.4% 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 Wed Dec 21 2011 at 14:22:07 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1906 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 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: 1.833508 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): -23.64600 34.60300 ymin,ymax (A): -19.12200 20.44400 zmin,zma (A): -3.341000 39.07900 x,y,z range (A): 58.24900 39.56600 42.42000 scale (grids/A): 1.833508 object centre (A): 5.478500 0.6610003 17.86900 number of atom coordinates read : 1906 total number of charged atoms : 1774 net assigned charge : 8.0009013E-02 assigned positive charge : 282.5200 centred at (gu) : 89.37547 91.01059 90.90907 assigned negative charge : -282.4403 centred at (gu) : 89.38447 91.18269 91.19614 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 52435 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17404 grid for indexing accessible points = 1.400000 m= 18366 mr = 35605 m= 2360 mr = 13386 m= 93 mr = 1301 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 22948 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 13849 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) : 0.6111693 object centre at (A) : 5.478500 0.6610003 17.86900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9461070E-03 -3.8419818E-03 midg,1,midg; midg,igrid,midg 1.8524404E-03 -5.0722429E-04 1,midg,midg; igrid,midg,midg 3.1359021E-02 2.1509469E-02 gauss-seidel spectral radius is 0.9984496 estimated iterations to convergence 201 setup time was (sec) 0.7800000 now iterating at: 14:22:09 rms-change max change #iterations 3.332937 159.2434 at 10iterations 1.478428 63.51544 at 20iterations 0.6576700 27.12193 at 30iterations 0.2921584 10.99378 at 40iterations 0.1303143 6.328133 at 50iterations 5.8112338E-02 2.249451 at 60iterations 2.5881315E-02 1.006485 at 70iterations 1.1466303E-02 0.3999896 at 80iterations 5.1022307E-03 0.1914368 at 90iterations 2.2807762E-03 8.8439941E-02 at 100iterations 1.0182661E-03 4.1984558E-02 at 110iterations 4.5320694E-04 1.6114712E-02 at 120iterations finished qdiffx linear iterations at : 14:22:20 total time elapsed so far: 11.62000 # loops : 120 mean,max change (kT/e) : 4.5320694E-04 1.6114712E-02 energy calculations done at 11.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.82000 DelPhi exited at 14:22:23 11.819u 0.338s 0:16.17 75.0% 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 Wed Dec 21 2011 at 14:22:25 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1906 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 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: 2.750262 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): -23.64600 34.60300 ymin,ymax (A): -19.12200 20.44400 zmin,zma (A): -3.341000 39.07900 x,y,z range (A): 58.24900 39.56600 42.42000 scale (grids/A): 2.750262 object centre (A): 5.478500 0.6610003 17.86900 number of atom coordinates read : 1906 total number of charged atoms : 1774 net assigned charge : 8.0009013E-02 assigned positive charge : 282.5200 centred at (gu) : 89.06316 91.51591 91.36366 assigned negative charge : -282.4403 centred at (gu) : 89.07672 91.77406 91.79434 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 120996 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17404 grid for indexing accessible points = 1.400000 m= 60349 mr = 86058 m= 20375 mr = 49213 m= 3843 mr = 16033 m= 380 mr = 2700 m= 10 mr = 209 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.200000 number of dielectric boundary points 51738 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 14192 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) : 1.833508 object centre at (A) : 5.478500 0.6610003 17.86900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1807659E-02 3.8956718E-03 midg,1,midg; midg,igrid,midg 1.7050778E-02 2.9361518E-02 1,midg,midg; igrid,midg,midg 0.5577807 0.2705274 gauss-seidel spectral radius is 0.9991932 estimated iterations to convergence 278 setup time was (sec) 1.510000 now iterating at: 14:22:27 rms-change max change #iterations 8.018278 346.8716 at 10iterations 4.599595 122.0887 at 20iterations 2.618171 62.45136 at 30iterations 1.482350 33.63033 at 40iterations 0.8380747 18.96550 at 50iterations 0.4710681 10.16713 at 60iterations 0.2652685 6.246277 at 70iterations 0.1494075 3.514630 at 80iterations 8.3867274E-02 1.839371 at 90iterations 4.7057051E-02 1.029545 at 100iterations 2.6437826E-02 0.6259500 at 110iterations 1.4839372E-02 0.3486301 at 120iterations 8.3041154E-03 0.1839461 at 130iterations 4.6454421E-03 0.1073837 at 140iterations 2.6062995E-03 6.1139107E-02 at 150iterations 1.4623649E-03 3.1499267E-02 at 160iterations 8.1874081E-04 1.8768311E-02 at 170iterations 4.5902820E-04 9.7780228E-03 at 180iterations finished qdiffx linear iterations at : 14:22:42 total time elapsed so far: 16.29000 # loops : 180 mean,max change (kT/e) : 4.5902820E-04 9.7780228E-03 energy calculations done at 16.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.48000 DelPhi exited at 14:22:47 16.482u 0.432s 0:22.33 75.7% 0+0k 0+0io 0pf+0w