Sun Oct 9 19:42:51 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 19:42:51 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5305 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5181498 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): 3.277000 68.35300 ymin,ymax (A): -8.944000 52.29000 zmin,zma (A): -1.704000 67.00200 x,y,z range (A): 65.07600 61.23400 68.70600 scale (grids/A): 0.5181498 object centre (A): 35.81500 21.67300 32.64900 number of atom coordinates read : 5305 total number of charged atoms : 5138 net assigned charge : 6.530044 assigned positive charge : 813.8874 centred at (gu) : 88.15979 89.69115 88.79004 assigned negative charge : -807.3635 centred at (gu) : 88.04291 89.71128 88.70969 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 9129 nv = 96 ne = 84 npr = 107569 no. pairs analyzed = 107569 no. exposed pairs = 6091 no. arc points = 41772 no. surface atoms = 2072 nbur = 3233 mkacc time = 0.2700000 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 = 1.652000 m= 328 mr = 5146 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 4299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4183 ## 574 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 12229 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5438127E-10 3.3682879E-10 midg,1,midg; midg,igrid,midg 2.4131430E-10 5.7354864E-11 1,midg,midg; igrid,midg,midg -5.4854415E-10 3.7480133E-10 gauss-seidel spectral radius is 0.9809797 estimated iterations to convergence 60 setup time was (sec) 0.7600000 now iterating at: 19:42:52 rms-change max change #iterations 8.0956168E-02 11.87378 at 10iterations 9.7096395E-03 1.519924 at 20iterations 3.5752356E-03 0.5873070 at 30iterations 1.4960964E-03 0.2470016 at 40iterations 6.3125376E-04 0.1035690 at 50iterations finished qdiffx linear iterations at : 19:42:54 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 6.3125376E-04 0.1035690 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 19:42:55 3.536u 0.157s 0:03.96 92.9% 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 Sun Oct 9 2011 at 19:42:55 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5305 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.554449 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): 3.277000 68.35300 ymin,ymax (A): -8.944000 52.29000 zmin,zma (A): -1.704000 67.00200 x,y,z range (A): 65.07600 61.23400 68.70600 scale (grids/A): 1.554449 object centre (A): 35.81500 21.67300 32.64900 number of atom coordinates read : 5305 total number of charged atoms : 5138 net assigned charge : 6.530044 assigned positive charge : 813.8874 centred at (gu) : 84.47795 89.07189 86.36877 assigned negative charge : -807.3635 centred at (gu) : 84.12885 89.13362 86.12914 start vw surface at 0.2200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 104105 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41772 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 33404 mr = 75414 m= 3155 mr = 23550 m= 68 mr = 1474 m= 0 mr = 10 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7500000 number of dielectric boundary points 40284 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 545 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 38810 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) : 0.5181498 object centre at (A) : 35.81500 21.67300 32.64900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6600363E-02 2.6521431E-02 midg,1,midg; midg,igrid,midg 1.4855876E-02 5.8094501E-03 1,midg,midg; igrid,midg,midg -1.0914777E-02 1.1896511E-02 gauss-seidel spectral radius is 0.9982071 estimated iterations to convergence 188 setup time was (sec) 1.050000 now iterating at: 19:42:56 rms-change max change #iterations 4.208642 149.6913 at 10iterations 1.763430 57.63189 at 20iterations 0.7433847 21.55178 at 30iterations 0.3126899 9.034979 at 40iterations 0.1323834 4.350300 at 50iterations 5.7048205E-02 1.750534 at 60iterations 2.5480710E-02 0.7947769 at 70iterations 1.2587616E-02 0.4360466 at 80iterations 7.2042104E-03 0.2558556 at 90iterations 4.6861917E-03 0.1566200 at 100iterations 3.3021434E-03 0.1082916 at 110iterations 2.4063461E-03 7.9322815E-02 at 120iterations finished qdiffx linear iterations at : 19:43:02 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 2.4063461E-03 7.9322815E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 19:43:03 7.680u 0.162s 0:08.11 96.6% 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 19:43:03 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5305 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.331674 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): 3.277000 68.35300 ymin,ymax (A): -8.944000 52.29000 zmin,zma (A): -1.704000 67.00200 x,y,z range (A): 65.07600 61.23400 68.70600 scale (grids/A): 2.331674 object centre (A): 35.81500 21.67300 32.64900 number of atom coordinates read : 5305 total number of charged atoms : 5138 net assigned charge : 6.530044 assigned positive charge : 813.8874 centred at (gu) : 81.71650 88.60754 84.55281 assigned negative charge : -807.3635 centred at (gu) : 81.19315 88.70028 84.19363 start vw surface at 0.2300000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 242686 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41772 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 116997 mr = 184049 m= 32461 mr = 94674 m= 4896 mr = 24434 m= 306 mr = 3170 m= 4 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.850000 number of dielectric boundary points 90878 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 40990 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) : 1.554449 object centre at (A) : 35.81500 21.67300 32.64900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3543414 0.7993758 midg,1,midg; midg,igrid,midg 0.2206682 4.9854953E-02 1,midg,midg; igrid,midg,midg -0.3459193 0.1825132 gauss-seidel spectral radius is 0.9991896 estimated iterations to convergence 277 setup time was (sec) 2.160000 now iterating at: 19:43:05 rms-change max change #iterations 11.14397 312.3361 at 10iterations 6.409834 145.6518 at 20iterations 3.653109 76.93742 at 30iterations 2.074625 42.63443 at 40iterations 1.176666 20.88585 at 50iterations 0.6651822 12.01873 at 60iterations 0.3755470 6.593109 at 70iterations 0.2118107 3.832196 at 80iterations 0.1196438 2.133682 at 90iterations 6.7836449E-02 1.181797 at 100iterations 3.8759269E-02 0.6597452 at 110iterations 2.2498909E-02 0.3951569 at 120iterations 1.3520577E-02 0.2607651 at 130iterations 8.5374545E-03 0.1635799 at 140iterations 5.7450971E-03 0.1244507 at 150iterations 4.1502062E-03 8.6353302E-02 at 160iterations 3.1722703E-03 6.5856934E-02 at 170iterations 2.5119709E-03 4.9713135E-02 at 180iterations finished qdiffx linear iterations at : 19:43:16 total time elapsed so far: 12.59000 # loops : 180 mean,max change (kT/e) : 2.5119709E-03 4.9713135E-02 energy calculations done at 12.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 19:43:16 12.793u 0.174s 0:13.33 97.2% 0+0k 0+0io 0pf+0w