Tue Oct 11 06:12:11 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 Tue Oct 11 2011 at 06:12:11 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2077 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7231069 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): 0.5159999 46.42000 ymin,ymax (A): 0.5749999 41.42700 zmin,zma (A): -2.019000 47.21300 x,y,z range (A): 45.90400 40.85200 49.23200 scale (grids/A): 0.7231069 object centre (A): 23.46800 21.00100 22.59700 number of atom coordinates read : 2077 total number of charged atoms : 1947 net assigned charge : 7.025011 assigned positive charge : 317.5371 centred at (gu) : 91.35783 90.24476 90.35592 assigned negative charge : -310.5121 centred at (gu) : 91.55451 90.23211 90.39768 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7495 nv = 96 ne = 84 npr = 41656 no. pairs analyzed = 41656 no. exposed pairs = 2493 no. arc points = 17038 no. surface atoms = 849 nbur = 1228 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 524 mr = 4421 m= 3 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3495 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1560 ## 136 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8008 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0862576E-07 6.2199533E-08 midg,1,midg; midg,igrid,midg 7.5152585E-08 1.0054527E-07 1,midg,midg; igrid,midg,midg 1.7060816E-07 -6.8905017E-08 gauss-seidel spectral radius is 0.9900261 estimated iterations to convergence 81 setup time was (sec) 0.4800000 now iterating at: 06:12:11 rms-change max change #iterations 0.2230420 33.68511 at 10iterations 2.9987214E-02 5.241967 at 20iterations 4.2095226E-03 0.6026421 at 30iterations 8.1708375E-04 9.5678329E-02 at 40iterations 2.3731425E-04 3.1661034E-02 at 50iterations finished qdiffx linear iterations at : 06:12:14 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 2.3731425E-04 3.1661034E-02 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 06:12:15 3.080u 0.145s 0:04.03 79.9% 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 Tue Oct 11 2011 at 06:12:15 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2077 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.169321 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): 0.5159999 46.42000 ymin,ymax (A): 0.5749999 41.42700 zmin,zma (A): -2.019000 47.21300 x,y,z range (A): 45.90400 40.85200 49.23200 scale (grids/A): 2.169321 object centre (A): 23.46800 21.00100 22.59700 number of atom coordinates read : 2077 total number of charged atoms : 1947 net assigned charge : 7.025011 assigned positive charge : 317.5371 centred at (gu) : 94.07347 90.73445 91.06800 assigned negative charge : -310.5121 centred at (gu) : 94.66360 90.69617 91.19292 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 78996 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17038 grid for indexing accessible points = 1.400000 m= 32761 mr = 56902 m= 6637 mr = 25293 m= 621 mr = 4573 m= 7 mr = 294 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 31960 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 15472 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) : 0.7231069 object centre at (A) : 23.46800 21.00100 22.59700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6303110E-02 6.6894025E-02 midg,1,midg; midg,igrid,midg 8.1285331E-03 3.4606919E-02 1,midg,midg; igrid,midg,midg 4.2265624E-02 -7.3579270E-03 gauss-seidel spectral radius is 0.9988728 estimated iterations to convergence 236 setup time was (sec) 0.8300000 now iterating at: 06:12:16 rms-change max change #iterations 4.841206 267.0645 at 10iterations 2.431814 84.86156 at 20iterations 1.223482 35.47868 at 30iterations 0.6165733 18.15252 at 40iterations 0.3098909 8.785962 at 50iterations 0.1563830 4.464699 at 60iterations 7.8750029E-02 2.299183 at 70iterations 3.9887283E-02 1.127190 at 80iterations 2.0138562E-02 0.6299124 at 90iterations 1.0341874E-02 0.2872009 at 100iterations 5.2927500E-03 0.1614380 at 110iterations 2.7766947E-03 8.3045959E-02 at 120iterations finished qdiffx linear iterations at : 06:12:22 total time elapsed so far: 6.760000 # loops : 120 mean,max change (kT/e) : 2.7766947E-03 8.3045959E-02 energy calculations done at 6.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.930000 DelPhi exited at 06:12:22 6.928u 0.181s 0:07.59 93.5% 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 06:12:22 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2077 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.253981 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): 0.5159999 46.42000 ymin,ymax (A): 0.5749999 41.42700 zmin,zma (A): -2.019000 47.21300 x,y,z range (A): 45.90400 40.85200 49.23200 scale (grids/A): 3.253981 object centre (A): 23.46800 21.00100 22.59700 number of atom coordinates read : 2077 total number of charged atoms : 1947 net assigned charge : 7.025011 assigned positive charge : 317.5371 centred at (gu) : 96.11015 91.10159 91.60202 assigned negative charge : -310.5121 centred at (gu) : 96.99535 91.04421 91.78948 start vw surface at 0.1400000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 182077 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17038 grid for indexing accessible points = 1.400000 m= 101177 mr = 136473 m= 42422 mr = 85052 m= 12684 mr = 35475 m= 2570 mr = 9940 m= 272 mr = 1932 m= 12 mr = 159 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.780000 number of dielectric boundary points 72183 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 15576 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) : 2.169321 object centre at (A) : 23.46800 21.00100 22.59700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4796852 0.7561991 midg,1,midg; midg,igrid,midg 6.0693147E-03 0.2683720 1,midg,midg; igrid,midg,midg 0.2974910 9.8940596E-02 gauss-seidel spectral radius is 0.9993047 estimated iterations to convergence 299 setup time was (sec) 2.060000 now iterating at: 06:12:25 rms-change max change #iterations 10.66673 486.1182 at 10iterations 6.347768 187.3745 at 20iterations 3.757188 78.12077 at 30iterations 2.224348 42.69684 at 40iterations 1.313793 27.04436 at 50iterations 0.7736509 15.31414 at 60iterations 0.4566376 8.686920 at 70iterations 0.2685280 5.048625 at 80iterations 0.1582263 2.944689 at 90iterations 9.2984311E-02 1.631565 at 100iterations 5.4850712E-02 1.109005 at 110iterations 3.2465905E-02 0.5781665 at 120iterations 1.9325254E-02 0.3294983 at 130iterations 1.1716755E-02 0.2075958 at 140iterations 7.2945128E-03 0.1263313 at 150iterations 4.7256011E-03 7.8029633E-02 at 160iterations 3.2492597E-03 5.2291870E-02 at 170iterations 2.3805562E-03 3.8633347E-02 at 180iterations finished qdiffx linear iterations at : 06:12:34 total time elapsed so far: 11.49000 # loops : 180 mean,max change (kT/e) : 2.3805562E-03 3.8633347E-02 energy calculations done at 11.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.66000 DelPhi exited at 06:12:35 11.661u 0.162s 0:12.15 97.2% 0+0k 0+0io 0pf+0w