Tue Oct 11 08:32:16 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 Tue Oct 11 2011 at 08:32:16 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 = 2051 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: 0.7152328 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): -4.279000 45.49500 ymin,ymax (A): 38.48700 85.61500 zmin,zma (A): -13.50100 28.76200 x,y,z range (A): 49.77400 47.12800 42.26300 scale (grids/A): 0.7152328 object centre (A): 20.60800 62.05100 7.630499 number of atom coordinates read : 2051 total number of charged atoms : 1992 net assigned charge : 6.500009 assigned positive charge : 322.2599 centred at (gu) : 90.77745 90.95493 90.28002 assigned negative charge : -315.7602 centred at (gu) : 90.72200 90.85986 90.35407 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7296 nv = 96 ne = 84 npr = 39759 no. pairs analyzed = 39759 no. exposed pairs = 2522 no. arc points = 17315 no. surface atoms = 872 nbur = 1179 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 505 mr = 4231 m= 2 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3486 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1674 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8127 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0303053E-07 2.1677749E-08 midg,1,midg; midg,igrid,midg 7.2849020E-09 1.4534103E-07 1,midg,midg; igrid,midg,midg 2.7904900E-08 1.1339363E-07 gauss-seidel spectral radius is 0.9898077 estimated iterations to convergence 81 setup time was (sec) 0.3600000 now iterating at: 08:32:16 rms-change max change #iterations 0.2104807 30.42495 at 10iterations 2.6876513E-02 3.419607 at 20iterations 3.5343163E-03 0.5517187 at 30iterations 5.4143649E-04 7.4334621E-02 at 40iterations 1.1861067E-04 1.5930176E-02 at 50iterations finished qdiffx linear iterations at : 08:32:19 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.1861067E-04 1.5930176E-02 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 08:32:20 3.383u 0.167s 0:03.86 91.7% 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 Tue Oct 11 2011 at 08:32:20 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 = 2051 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: 2.145699 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): -4.279000 45.49500 ymin,ymax (A): 38.48700 85.61500 zmin,zma (A): -13.50100 28.76200 x,y,z range (A): 49.77400 47.12800 42.26300 scale (grids/A): 2.145699 object centre (A): 20.60800 62.05100 7.630499 number of atom coordinates read : 2051 total number of charged atoms : 1992 net assigned charge : 6.500009 assigned positive charge : 322.2599 centred at (gu) : 92.33247 92.86470 90.84000 assigned negative charge : -315.7602 centred at (gu) : 92.16615 92.57956 91.06243 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 77139 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17315 grid for indexing accessible points = 1.400000 m= 31188 mr = 54903 m= 5966 mr = 23695 m= 531 mr = 3929 m= 19 mr = 279 m= 0 mr = 3 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 32034 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 15818 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) : 0.7152328 object centre at (A) : 20.60800 62.05100 7.630499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6711643E-02 2.5660599E-02 midg,1,midg; midg,igrid,midg -3.4697179E-02 2.9292636E-02 1,midg,midg; igrid,midg,midg 4.7999144E-02 5.3683449E-02 gauss-seidel spectral radius is 0.9988528 estimated iterations to convergence 234 setup time was (sec) 0.6000000 now iterating at: 08:32:21 rms-change max change #iterations 4.690102 236.1834 at 10iterations 2.327913 84.28275 at 20iterations 1.166073 35.77525 at 30iterations 0.5820757 20.11734 at 40iterations 0.2910166 8.445938 at 50iterations 0.1449258 4.253033 at 60iterations 7.2659880E-02 2.192088 at 70iterations 3.6485668E-02 1.063078 at 80iterations 1.8284518E-02 0.5345268 at 90iterations 9.2150588E-03 0.2582851 at 100iterations 4.6610641E-03 0.1523514 at 110iterations 2.4056276E-03 7.0426948E-02 at 120iterations finished qdiffx linear iterations at : 08:32:28 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 2.4056276E-03 7.0426948E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 08:32:28 7.865u 0.196s 0:08.43 95.4% 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 Tue Oct 11 2011 at 08:32:28 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 = 2051 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: 3.218548 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): -4.279000 45.49500 ymin,ymax (A): 38.48700 85.61500 zmin,zma (A): -13.50100 28.76200 x,y,z range (A): 49.77400 47.12800 42.26300 scale (grids/A): 3.218548 object centre (A): 20.60800 62.05100 7.630499 number of atom coordinates read : 2051 total number of charged atoms : 1992 net assigned charge : 6.500009 assigned positive charge : 322.2599 centred at (gu) : 93.49872 94.29694 91.25995 assigned negative charge : -315.7602 centred at (gu) : 93.24927 93.86935 91.59361 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 177855 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17315 grid for indexing accessible points = 1.400000 m= 97342 mr = 132168 m= 39427 mr = 81249 m= 11195 mr = 32306 m= 2294 mr = 8637 m= 294 mr = 1662 m= 14 mr = 194 m= 0 mr = 0 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 72205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 15936 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) : 2.145699 object centre at (A) : 20.60800 62.05100 7.630499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1741085 0.2224944 midg,1,midg; midg,igrid,midg -0.4149829 0.2538669 1,midg,midg; igrid,midg,midg 0.2643732 0.4533447 gauss-seidel spectral radius is 0.9993063 estimated iterations to convergence 300 setup time was (sec) 1.410000 now iterating at: 08:32:30 rms-change max change #iterations 10.41336 398.6178 at 10iterations 6.152217 134.1640 at 20iterations 3.638000 64.07461 at 30iterations 2.150479 41.16489 at 40iterations 1.265333 24.86860 at 50iterations 0.7449287 13.76039 at 60iterations 0.4388586 7.746407 at 70iterations 0.2579345 4.797890 at 80iterations 0.1516290 2.629831 at 90iterations 8.9129910E-02 1.622556 at 100iterations 5.2550331E-02 0.9453068 at 110iterations 3.1029804E-02 0.5751266 at 120iterations 1.8438470E-02 0.3441010 at 130iterations 1.1102902E-02 0.1882286 at 140iterations 6.8337759E-03 0.1236153 at 150iterations 4.3499544E-03 8.4365845E-02 at 160iterations 2.9186581E-03 5.6314468E-02 at 170iterations 2.0721017E-03 3.8978577E-02 at 180iterations finished qdiffx linear iterations at : 08:32:41 total time elapsed so far: 12.61000 # loops : 180 mean,max change (kT/e) : 2.0721017E-03 3.8978577E-02 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.74000 DelPhi exited at 08:32:42 12.739u 0.211s 0:13.24 97.7% 0+0k 0+0io 0pf+0w