Sun Oct 9 03:33:46 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 Sun Oct 9 2011 at 03:33:47 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4567 !!! WARNING: HIZ 910 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 4 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4205254 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): -3.394000 54.34400 ymin,ymax (A): -84.88800 -18.07900 zmin,zma (A): -14.33700 70.31900 x,y,z range (A): 57.73800 66.80900 84.65600 scale (grids/A): 0.4205254 object centre (A): 25.47500 -51.48350 27.99100 number of atom coordinates read : 4567 total number of charged atoms : 4380 net assigned charge : 19.99999 assigned positive charge : 675.7279 centred at (gu) : 89.73618 88.16129 93.65612 assigned negative charge : -655.7328 centred at (gu) : 89.71131 88.16138 93.71258 start vw surface at 0.2100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 4895 nv = 96 ne = 84 npr = 90125 no. pairs analyzed = 90125 no. exposed pairs = 5938 no. arc points = 41311 no. surface atoms = 2008 nbur = 2559 mkacc time = 0.2000000 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 = 2.016000 m= 129 mr = 2293 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 0.4300000 number of dielectric boundary points 2731 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3265 ## 714 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 6631 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1109139E-12 2.8675888E-12 midg,1,midg; midg,igrid,midg 3.8895328E-12 1.2489167E-12 1,midg,midg; igrid,midg,midg 1.7901239E-12 2.5112293E-12 gauss-seidel spectral radius is 0.9711930 estimated iterations to convergence 49 setup time was (sec) 0.6400000 now iterating at: 03:33:47 rms-change max change #iterations 2.5498372E-02 5.422674 at 10iterations 3.3562910E-03 0.6035633 at 20iterations 9.0210268E-04 0.1756058 at 30iterations 2.5187817E-04 5.0399780E-02 at 40iterations 7.0853523E-05 1.4331818E-02 at 50iterations finished qdiffx linear iterations at : 03:33:50 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 7.0853523E-05 1.4331818E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 03:33:50 3.314u 0.172s 0:03.75 92.8% 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 Sun Oct 9 2011 at 03:33:50 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4567 !!! WARNING: HIZ 910 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 4 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.261576 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): -3.394000 54.34400 ymin,ymax (A): -84.88800 -18.07900 zmin,zma (A): -14.33700 70.31900 x,y,z range (A): 57.73800 66.80900 84.65600 scale (grids/A): 1.261576 object centre (A): 25.47500 -51.48350 27.99100 number of atom coordinates read : 4567 total number of charged atoms : 4380 net assigned charge : 19.99999 assigned positive charge : 675.7279 centred at (gu) : 89.20663 84.48245 100.9669 assigned negative charge : -655.7328 centred at (gu) : 89.13374 84.48365 101.1374 start vw surface at 0.1900000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 57712 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41311 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.876000 m= 13079 mr = 37755 m= 594 mr = 7698 m= 4 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 54 time to turn everything in is 0.4600000 number of dielectric boundary points 25846 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 745 ## 31 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 30121 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) : 0.4205254 object centre at (A) : 25.47500 -51.48350 27.99100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6651542E-03 1.5147943E-02 midg,1,midg; midg,igrid,midg 3.7612088E-03 1.8670557E-03 1,midg,midg; igrid,midg,midg 1.2173774E-03 1.0222973E-03 gauss-seidel spectral radius is 0.9970422 estimated iterations to convergence 147 setup time was (sec) 0.7400000 now iterating at: 03:33:51 rms-change max change #iterations 2.231073 107.0952 at 10iterations 0.7297956 34.88264 at 20iterations 0.2404603 9.450779 at 30iterations 7.9577215E-02 3.625082 at 40iterations 2.6782259E-02 1.162062 at 50iterations 9.6040359E-03 0.4667692 at 60iterations 4.0011341E-03 0.1902771 at 70iterations 2.0521486E-03 9.3383789E-02 at 80iterations 1.2369718E-03 5.4790497E-02 at 90iterations 7.8666297E-04 3.4358978E-02 at 100iterations 5.1059638E-04 2.2502899E-02 at 110iterations 3.3383109E-04 1.4793396E-02 at 120iterations finished qdiffx linear iterations at : 03:33:58 total time elapsed so far: 7.180000 # loops : 120 mean,max change (kT/e) : 3.3383109E-04 1.4793396E-02 energy calculations done at 7.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.360000 DelPhi exited at 03:33:58 7.359u 0.204s 0:07.85 96.1% 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 Sun Oct 9 2011 at 03:33:58 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4567 !!! WARNING: HIZ 910 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 4 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.892364 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): -3.394000 54.34400 ymin,ymax (A): -84.88800 -18.07900 zmin,zma (A): -14.33700 70.31900 x,y,z range (A): 57.73800 66.80900 84.65600 scale (grids/A): 1.892364 object centre (A): 25.47500 -51.48350 27.99100 number of atom coordinates read : 4567 total number of charged atoms : 4380 net assigned charge : 19.99999 assigned positive charge : 675.7279 centred at (gu) : 88.80968 81.72321 106.4499 assigned negative charge : -655.7328 centred at (gu) : 88.70049 81.72556 106.7061 start vw surface at 0.2000000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 135732 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41311 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.848000 m= 51140 mr = 94624 m= 8751 mr = 37543 m= 552 mr = 5392 m= 6 mr = 178 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 212 time to turn everything in is 1.010000 number of dielectric boundary points 58444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 231 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 34452 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) : 1.261576 object centre at (A) : 25.47500 -51.48350 27.99100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0922068E-02 0.4149346 midg,1,midg; midg,igrid,midg 0.1036782 5.1072247E-02 1,midg,midg; igrid,midg,midg 3.0609740E-02 2.5759455E-02 gauss-seidel spectral radius is 0.9987803 estimated iterations to convergence 227 setup time was (sec) 1.300000 now iterating at: 03:34:00 rms-change max change #iterations 6.891955 218.2286 at 10iterations 3.493535 100.9526 at 20iterations 1.760524 56.53559 at 30iterations 0.8802505 23.36835 at 40iterations 0.4382251 12.68841 at 50iterations 0.2178538 6.605631 at 60iterations 0.1076076 2.709545 at 70iterations 5.3218827E-02 1.319290 at 80iterations 2.6293771E-02 0.7269764 at 90iterations 1.2980377E-02 0.3289671 at 100iterations 6.4560589E-03 0.1771569 at 110iterations 3.2447015E-03 8.3703995E-02 at 120iterations 1.6637120E-03 4.3994904E-02 at 130iterations 8.9199567E-04 2.5274277E-02 at 140iterations 5.0796929E-04 1.4303207E-02 at 150iterations 3.1438153E-04 8.3899498E-03 at 160iterations 2.0958565E-04 5.7296753E-03 at 170iterations 1.4707711E-04 3.7555695E-03 at 180iterations finished qdiffx linear iterations at : 03:34:10 total time elapsed so far: 11.60000 # loops : 180 mean,max change (kT/e) : 1.4707711E-04 3.7555695E-03 energy calculations done at 11.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.77000 DelPhi exited at 03:34:11 11.772u 0.219s 0:12.26 97.7% 0+0k 0+0io 0pf+0w