Sat Oct 15 14:32:20 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+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 Sat Oct 15 2011 at 14:32:20 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2870 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 0.5821940 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): -30.37100 30.77700 ymin,ymax (A): 11.01300 57.65500 zmin,zma (A): -1.607000 46.43800 x,y,z range (A): 61.14800 46.64200 48.04500 scale (grids/A): 0.5821940 object centre (A): 0.2030001 34.33400 22.41550 number of atom coordinates read : 2870 total number of charged atoms : 2730 net assigned charge : 0.5140209 assigned positive charge : 436.0851 centred at (gu) : 90.79559 90.13907 90.68314 assigned negative charge : -435.5722 centred at (gu) : 90.78372 90.32996 90.77962 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6361 nv = 96 ne = 84 npr = 57370 no. pairs analyzed = 57370 no. exposed pairs = 3681 no. arc points = 25809 no. surface atoms = 1245 nbur = 1625 mkacc time = 0.1000000 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 = 1.484000 m= 279 mr = 3286 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.2200000 number of dielectric boundary points 3335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2639 ## 321 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8129 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0077711E-09 -2.4890181E-09 midg,1,midg; midg,igrid,midg 4.3284971E-09 -4.5249338E-09 1,midg,midg; igrid,midg,midg -1.0415677E-10 5.1015736E-10 gauss-seidel spectral radius is 0.9847645 estimated iterations to convergence 67 setup time was (sec) 0.4200000 now iterating at: 14:32:20 rms-change max change #iterations 9.9574976E-02 15.56322 at 10iterations 7.7512800E-03 1.176977 at 20iterations 6.2657928E-04 0.1036911 at 30iterations 4.9145925E-05 7.2097778E-03 at 40iterations 4.0638593E-06 5.9509277E-04 at 50iterations finished qdiffx linear iterations at : 14:32:25 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 4.0638593E-06 5.9509277E-04 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 14:32:26 3.662u 0.205s 0:05.87 65.7% 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 Sat Oct 15 2011 at 14:32:26 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2870 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 1.746582 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): -30.37100 30.77700 ymin,ymax (A): 11.01300 57.65500 zmin,zma (A): -1.607000 46.43800 x,y,z range (A): 61.14800 46.64200 48.04500 scale (grids/A): 1.746582 object centre (A): 0.2030001 34.33400 22.41550 number of atom coordinates read : 2870 total number of charged atoms : 2730 net assigned charge : 0.5140209 assigned positive charge : 436.0851 centred at (gu) : 92.38604 90.41669 92.04855 assigned negative charge : -435.5722 centred at (gu) : 92.35098 90.98950 92.33845 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 69596 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25809 grid for indexing accessible points = 1.400000 m= 22487 mr = 46811 m= 2705 mr = 15628 m= 102 mr = 1366 m= 0 mr = 25 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1264 time to turn everything in is 0.3500000 number of dielectric boundary points 31060 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 221 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 21250 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) : 0.5821940 object centre at (A) : 0.2030001 34.33400 22.41550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9294656E-03 -6.4039966E-03 midg,1,midg; midg,igrid,midg 1.6894596E-02 -2.5546914E-02 1,midg,midg; igrid,midg,midg 5.1352382E-03 6.1743166E-03 gauss-seidel spectral radius is 0.9984093 estimated iterations to convergence 199 setup time was (sec) 0.5800000 now iterating at: 14:32:26 rms-change max change #iterations 3.793605 178.3730 at 10iterations 1.661925 56.80663 at 20iterations 0.7300282 24.92125 at 30iterations 0.3220456 11.76401 at 40iterations 0.1415803 4.768666 at 50iterations 6.2472049E-02 2.101078 at 60iterations 2.7452793E-02 0.9015656 at 70iterations 1.2110735E-02 0.4121847 at 80iterations 5.3440500E-03 0.1708684 at 90iterations 2.3497029E-03 8.4014893E-02 at 100iterations 1.0379783E-03 3.1654358E-02 at 110iterations 4.5585269E-04 1.5228629E-02 at 120iterations finished qdiffx linear iterations at : 14:32:37 total time elapsed so far: 8.180000 # loops : 120 mean,max change (kT/e) : 4.5585269E-04 1.5228629E-02 energy calculations done at 8.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.310000 DelPhi exited at 14:32:37 8.308u 0.274s 0:11.51 74.4% 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 Sat Oct 15 2011 at 14:32:37 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2870 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 2.619873 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): -30.37100 30.77700 ymin,ymax (A): 11.01300 57.65500 zmin,zma (A): -1.607000 46.43800 x,y,z range (A): 61.14800 46.64200 48.04500 scale (grids/A): 2.619873 object centre (A): 0.2030001 34.33400 22.41550 number of atom coordinates read : 2870 total number of charged atoms : 2730 net assigned charge : 0.5140209 assigned positive charge : 436.0851 centred at (gu) : 93.57885 90.62466 93.07278 assigned negative charge : -435.5722 centred at (gu) : 93.52627 91.48418 93.50761 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 161124 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25809 grid for indexing accessible points = 1.400000 m= 75816 mr = 114268 m= 23794 mr = 60104 m= 4379 mr = 18177 m= 461 mr = 2823 m= 19 mr = 274 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 4380 time to turn everything in is 0.9200000 number of dielectric boundary points 69947 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 21831 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) : 1.746582 object centre at (A) : 0.2030001 34.33400 22.41550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6069467E-02 -6.4771213E-02 midg,1,midg; midg,igrid,midg 0.2297470 -0.2890415 1,midg,midg; igrid,midg,midg 5.6909844E-02 0.1249997 gauss-seidel spectral radius is 0.9992073 estimated iterations to convergence 280 setup time was (sec) 1.230000 now iterating at: 14:32:39 rms-change max change #iterations 9.572721 338.8738 at 10iterations 5.520220 131.2117 at 20iterations 3.151592 71.70870 at 30iterations 1.791860 46.05701 at 40iterations 1.016428 19.20306 at 50iterations 0.5758972 11.31009 at 60iterations 0.3256179 6.643697 at 70iterations 0.1841485 3.538437 at 80iterations 0.1036209 2.040062 at 90iterations 5.8502380E-02 1.154329 at 100iterations 3.2895569E-02 0.6219025 at 110iterations 1.8546185E-02 0.3749442 at 120iterations 1.0453178E-02 0.2078161 at 130iterations 5.8725290E-03 0.1217756 at 140iterations 3.3098410E-03 5.9835434E-02 at 150iterations 1.8614155E-03 3.7743211E-02 at 160iterations 1.0460494E-03 2.0677567E-02 at 170iterations 5.8981008E-04 1.1802673E-02 at 180iterations finished qdiffx linear iterations at : 14:33:02 total time elapsed so far: 13.39000 # loops : 180 mean,max change (kT/e) : 5.8981008E-04 1.1802673E-02 energy calculations done at 13.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.54000 DelPhi exited at 14:33:02 13.539u 0.290s 0:24.86 55.5% 0+0k 0+0io 0pf+0w