Wed Feb 15 08:55:40 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:40 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 = 2853 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5585189 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): -20.77800 31.89900 ymin,ymax (A): -33.66100 23.35300 zmin,zma (A): -6.438000 57.30200 x,y,z range (A): 52.67700 57.01400 63.74000 scale (grids/A): 0.5585189 object centre (A): 5.560500 -5.153999 25.43200 number of atom coordinates read : 2853 total number of charged atoms : 2728 net assigned charge : 2.500007 assigned positive charge : 414.4883 centred at (gu) : 88.80892 89.11561 90.63747 assigned negative charge : -411.9895 centred at (gu) : 88.68767 89.19777 90.53872 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5941 nv = 96 ne = 84 npr = 58256 no. pairs analyzed = 58256 no. exposed pairs = 3776 no. arc points = 26995 no. surface atoms = 1262 nbur = 1591 mkacc time = 0.1400000 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 = 1.540000 m= 222 mr = 2931 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.3400000 number of dielectric boundary points 3226 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2820 ## 362 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7721 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.1197281E-10 1.4044345E-09 midg,1,midg; midg,igrid,midg 1.2962795E-09 -4.4286849E-10 1,midg,midg; igrid,midg,midg -1.2720968E-09 1.0589961E-09 gauss-seidel spectral radius is 0.9834637 estimated iterations to convergence 64 setup time was (sec) 0.5900000 now iterating at: 08:55:41 rms-change max change #iterations 7.6255530E-02 12.28189 at 10iterations 5.5082859E-03 0.8882065 at 20iterations 4.2132504E-04 6.9703579E-02 at 30iterations 4.1725783E-05 6.5364838E-03 at 40iterations 6.0196735E-06 9.9945068E-04 at 50iterations finished qdiffx linear iterations at : 08:55:44 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 6.0196735E-06 9.9945068E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 08:55:44 3.493u 0.190s 0:04.33 84.9% 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 Feb 15 2012 at 08:55:45 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 = 2853 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: 1.675557 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): -20.77800 31.89900 ymin,ymax (A): -33.66100 23.35300 zmin,zma (A): -6.438000 57.30200 x,y,z range (A): 52.67700 57.01400 63.74000 scale (grids/A): 1.675557 object centre (A): 5.560500 -5.153999 25.43200 number of atom coordinates read : 2853 total number of charged atoms : 2728 net assigned charge : 2.500007 assigned positive charge : 414.4883 centred at (gu) : 86.42570 87.34616 91.91167 assigned negative charge : -411.9895 centred at (gu) : 86.06280 87.59309 91.61577 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 65076 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26995 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19469 mr = 42800 m= 2128 mr = 12982 m= 67 mr = 1042 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 395 time to turn everything in is 0.5200000 number of dielectric boundary points 29913 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 309 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 21023 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) : 0.5585189 object centre at (A) : 5.560500 -5.153999 25.43200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7111398E-02 1.0555796E-02 midg,1,midg; midg,igrid,midg 2.5587301E-03 -8.6249933E-03 1,midg,midg; igrid,midg,midg -4.5459559E-03 1.7517094E-02 gauss-seidel spectral radius is 0.9982761 estimated iterations to convergence 191 setup time was (sec) 0.8700000 now iterating at: 08:55:46 rms-change max change #iterations 3.351743 154.3549 at 10iterations 1.427052 64.25316 at 20iterations 0.6086555 23.12561 at 30iterations 0.2591732 8.981762 at 40iterations 0.1105652 4.006740 at 50iterations 4.7061365E-02 1.761288 at 60iterations 2.0073354E-02 0.7339706 at 70iterations 8.5509261E-03 0.2978592 at 80iterations 3.6462164E-03 0.1314373 at 90iterations 1.5616699E-03 5.6455612E-02 at 100iterations 6.6340488E-04 2.5135756E-02 at 110iterations 2.8406957E-04 1.0643244E-02 at 120iterations finished qdiffx linear iterations at : 08:55:53 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 2.8406957E-04 1.0643244E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.050000 DelPhi exited at 08:55:54 8.052u 0.261s 0:09.25 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 Wed Feb 15 2012 at 08:55:54 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 = 2853 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.513335 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): -20.77800 31.89900 ymin,ymax (A): -33.66100 23.35300 zmin,zma (A): -6.438000 57.30200 x,y,z range (A): 52.67700 57.01400 63.74000 scale (grids/A): 2.513335 object centre (A): 5.560500 -5.153999 25.43200 number of atom coordinates read : 2853 total number of charged atoms : 2728 net assigned charge : 2.500007 assigned positive charge : 414.4883 centred at (gu) : 84.63831 86.01900 92.86743 assigned negative charge : -411.9895 centred at (gu) : 84.09416 86.38970 92.42370 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 151345 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26995 grid for indexing accessible points = 1.400000 m= 66840 mr = 105510 m= 19511 mr = 51636 m= 3303 mr = 14363 m= 240 mr = 2149 m= 3 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 1299 time to turn everything in is 1.200000 number of dielectric boundary points 67484 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 21805 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) : 1.675557 object centre at (A) : 5.560500 -5.153999 25.43200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4423469 0.2341786 midg,1,midg; midg,igrid,midg 3.2589968E-02 -0.1032243 1,midg,midg; igrid,midg,midg -7.8055412E-02 0.2710525 gauss-seidel spectral radius is 0.9991691 estimated iterations to convergence 274 setup time was (sec) 1.510000 now iterating at: 08:55:56 rms-change max change #iterations 8.611588 387.6597 at 10iterations 4.886965 123.7063 at 20iterations 2.762330 61.00972 at 30iterations 1.550816 34.73057 at 40iterations 0.8676783 19.97600 at 50iterations 0.4860200 10.37074 at 60iterations 0.2705460 6.328390 at 70iterations 0.1509828 3.386822 at 80iterations 8.3975963E-02 1.782661 at 90iterations 4.6705045E-02 0.9693928 at 100iterations 2.6002165E-02 0.5347526 at 110iterations 1.4414294E-02 0.3073425 at 120iterations 8.0190115E-03 0.1637993 at 130iterations 4.4552740E-03 9.3585968E-02 at 140iterations 2.4743201E-03 4.8191309E-02 at 150iterations 1.3736867E-03 3.0419350E-02 at 160iterations 7.6238072E-04 1.6708374E-02 at 170iterations 4.2384668E-04 8.6479187E-03 at 180iterations finished qdiffx linear iterations at : 08:56:07 total time elapsed so far: 12.91000 # loops : 180 mean,max change (kT/e) : 4.2384668E-04 8.6479187E-03 energy calculations done at 12.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.10000 DelPhi exited at 08:56:09 13.103u 0.283s 0:15.39 86.9% 0+0k 0+0io 0pf+0w