Mon Oct 10 13:59:48 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 Mon Oct 10 2011 at 13:59:49 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 = 2858 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5787582 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): 18.15200 79.66300 ymin,ymax (A): 29.53100 85.94200 zmin,zma (A): -3.461000 49.11000 x,y,z range (A): 61.51100 56.41100 52.57100 scale (grids/A): 0.5787582 object centre (A): 48.90750 57.73650 22.82450 number of atom coordinates read : 2858 total number of charged atoms : 2708 net assigned charge : 9.000013 assigned positive charge : 418.0830 centred at (gu) : 88.53304 90.18958 87.62349 assigned negative charge : -409.0834 centred at (gu) : 88.39273 90.11799 87.49487 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6498 nv = 96 ne = 84 npr = 55625 no. pairs analyzed = 55625 no. exposed pairs = 4295 no. arc points = 30976 no. surface atoms = 1410 nbur = 1448 mkacc time = 0.1300000 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= 310 mr = 2913 m= 0 mr = 11 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2960 ## 279 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8065 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0456651E-09 2.5525839E-09 midg,1,midg; midg,igrid,midg 5.6734412E-10 3.4937193E-09 1,midg,midg; igrid,midg,midg -1.1381083E-09 3.2959431E-09 gauss-seidel spectral radius is 0.9845988 estimated iterations to convergence 66 setup time was (sec) 0.5600000 now iterating at: 13:59:49 rms-change max change #iterations 9.3307644E-02 18.16376 at 10iterations 7.1672336E-03 1.174587 at 20iterations 5.6280423E-04 9.2236876E-02 at 30iterations 4.7818430E-05 6.7386627E-03 at 40iterations 6.1872151E-06 7.5769424E-04 at 50iterations finished qdiffx linear iterations at : 13:59:52 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 6.1872151E-06 7.5769424E-04 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 13:59:53 3.393u 0.162s 0:04.22 84.1% 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 Mon Oct 10 2011 at 13:59:53 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 = 2858 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.736275 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): 18.15200 79.66300 ymin,ymax (A): 29.53100 85.94200 zmin,zma (A): -3.461000 49.11000 x,y,z range (A): 61.51100 56.41100 52.57100 scale (grids/A): 1.736275 object centre (A): 48.90750 57.73650 22.82450 number of atom coordinates read : 2858 total number of charged atoms : 2708 net assigned charge : 9.000013 assigned positive charge : 418.0830 centred at (gu) : 85.59862 90.56877 82.87002 assigned negative charge : -409.0834 centred at (gu) : 85.17796 90.35370 82.48435 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 69605 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30976 grid for indexing accessible points = 1.400000 m= 21815 mr = 43075 m= 2669 mr = 13988 m= 103 mr = 1151 m= 0 mr = 3 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 154 time to turn everything in is 0.5600000 number of dielectric boundary points 35975 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 270 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 21088 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) : 0.5787582 object centre at (A) : 48.90750 57.73650 22.82450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3030197E-02 1.6324384E-02 midg,1,midg; midg,igrid,midg -1.6749142E-02 3.7962619E-02 1,midg,midg; igrid,midg,midg -1.8576477E-02 2.1179074E-02 gauss-seidel spectral radius is 0.9984093 estimated iterations to convergence 199 setup time was (sec) 0.8800000 now iterating at: 13:59:54 rms-change max change #iterations 3.620707 177.3044 at 10iterations 1.582103 62.02703 at 20iterations 0.6952760 26.67926 at 30iterations 0.3052656 10.70427 at 40iterations 0.1347048 4.536578 at 50iterations 5.8879368E-02 2.160693 at 60iterations 2.5943909E-02 0.8839817 at 70iterations 1.1434590E-02 0.3818779 at 80iterations 5.0203884E-03 0.1866064 at 90iterations 2.2174199E-03 9.1979980E-02 at 100iterations 9.7456994E-04 3.4271240E-02 at 110iterations 4.2841907E-04 1.5960693E-02 at 120iterations finished qdiffx linear iterations at : 14:00:01 total time elapsed so far: 8.120000 # loops : 120 mean,max change (kT/e) : 4.2841907E-04 1.5960693E-02 energy calculations done at 8.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.340000 DelPhi exited at 14:00:02 8.344u 0.230s 0:08.93 95.9% 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 Mon Oct 10 2011 at 14:00:02 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 = 2858 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.604412 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): 18.15200 79.66300 ymin,ymax (A): 29.53100 85.94200 zmin,zma (A): -3.461000 49.11000 x,y,z range (A): 61.51100 56.41100 52.57100 scale (grids/A): 2.604412 object centre (A): 48.90750 57.73650 22.82450 number of atom coordinates read : 2858 total number of charged atoms : 2708 net assigned charge : 9.000013 assigned positive charge : 418.0830 centred at (gu) : 83.39780 90.85290 79.30479 assigned negative charge : -409.0834 centred at (gu) : 82.76690 90.53054 78.72648 start vw surface at 0.1700000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 161167 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30976 grid for indexing accessible points = 1.400000 m= 72341 mr = 106498 m= 22886 mr = 54267 m= 4081 mr = 16412 m= 268 mr = 2322 m= 5 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 537 time to turn everything in is 1.370000 number of dielectric boundary points 81165 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 21656 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) : 1.736275 object centre at (A) : 48.90750 57.73650 22.82450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1853744 0.1975303 midg,1,midg; midg,igrid,midg -0.3697385 0.5456395 1,midg,midg; igrid,midg,midg -0.2494957 0.2762827 gauss-seidel spectral radius is 0.9992217 estimated iterations to convergence 283 setup time was (sec) 1.730000 now iterating at: 14:00:04 rms-change max change #iterations 9.347757 291.9641 at 10iterations 5.539723 146.2148 at 20iterations 3.241792 85.41619 at 30iterations 1.875183 46.60447 at 40iterations 1.080500 28.64944 at 50iterations 0.6208344 16.46994 at 60iterations 0.3551136 9.160431 at 70iterations 0.2025866 4.581066 at 80iterations 0.1157137 2.934211 at 90iterations 6.5832488E-02 1.446922 at 100iterations 3.7429504E-02 0.8900414 at 110iterations 2.1286311E-02 0.4980316 at 120iterations 1.2074464E-02 0.2443047 at 130iterations 6.8544834E-03 0.1504440 at 140iterations 3.8848452E-03 9.0289116E-02 at 150iterations 2.2042505E-03 5.4746628E-02 at 160iterations 1.2468789E-03 2.8629303E-02 at 170iterations 7.0731773E-04 1.5839577E-02 at 180iterations finished qdiffx linear iterations at : 14:00:16 total time elapsed so far: 13.41000 # loops : 180 mean,max change (kT/e) : 7.0731773E-04 1.5839577E-02 energy calculations done at 13.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.61000 DelPhi exited at 14:00:16 13.609u 0.287s 0:14.30 97.0% 0+0k 0+0io 0pf+0w