Sun Oct 9 07:16:02 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 07:16:02 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 = 2537 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: 0.5515019 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): -5.246000 41.45700 ymin,ymax (A): 37.65300 89.36400 zmin,zma (A): -2.670000 61.88100 x,y,z range (A): 46.70300 51.71100 64.55099 scale (grids/A): 0.5515019 object centre (A): 18.10550 63.50850 29.60550 number of atom coordinates read : 2537 total number of charged atoms : 2391 net assigned charge : -9.499978 assigned positive charge : 379.0038 centred at (gu) : 90.98536 88.30129 89.45344 assigned negative charge : -388.5043 centred at (gu) : 91.16497 87.91314 89.38677 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5020 nv = 96 ne = 84 npr = 50880 no. pairs analyzed = 50880 no. exposed pairs = 3496 no. arc points = 24904 no. surface atoms = 1187 nbur = 1350 mkacc time = 0.1100000 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 = 1.540000 m= 216 mr = 2375 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2800000 number of dielectric boundary points 2858 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2515 ## 314 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6552 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2878095E-09 -1.6539267E-10 midg,1,midg; midg,igrid,midg -5.4072937E-09 1.2833230E-09 1,midg,midg; igrid,midg,midg 4.5560292E-10 -2.4887643E-09 gauss-seidel spectral radius is 0.9830169 estimated iterations to convergence 63 setup time was (sec) 0.5200000 now iterating at: 07:16:02 rms-change max change #iterations 6.9162458E-02 11.81384 at 10iterations 4.6299477E-03 0.9323559 at 20iterations 3.1747957E-04 5.8833838E-02 at 30iterations 2.1679547E-05 4.2347908E-03 at 40iterations 1.5364061E-06 2.9945374E-04 at 50iterations finished qdiffx linear iterations at : 07:16:05 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.5364061E-06 2.9945374E-04 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 07:16:06 3.358u 0.219s 0:03.87 91.9% 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 07:16:06 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 = 2537 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: 1.654506 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): -5.246000 41.45700 ymin,ymax (A): 37.65300 89.36400 zmin,zma (A): -2.670000 61.88100 x,y,z range (A): 46.70300 51.71100 64.55099 scale (grids/A): 1.654506 object centre (A): 18.10550 63.50850 29.60550 number of atom coordinates read : 2537 total number of charged atoms : 2391 net assigned charge : -9.499978 assigned positive charge : 379.0038 centred at (gu) : 92.95530 84.90320 88.35986 assigned negative charge : -388.5043 centred at (gu) : 93.49442 83.73925 88.16010 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 55516 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24904 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15846 mr = 35369 m= 1464 mr = 10472 m= 33 mr = 604 m= 0 mr = 3 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 834 time to turn everything in is 0.4100000 number of dielectric boundary points 26411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 274 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 18361 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) : 0.5515019 object centre at (A) : 18.10550 63.50850 29.60550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2741737E-02 3.7554007E-03 midg,1,midg; midg,igrid,midg -3.2826934E-02 5.7896026E-03 1,midg,midg; igrid,midg,midg -3.2071022E-03 -1.6549727E-02 gauss-seidel spectral radius is 0.9981813 estimated iterations to convergence 186 setup time was (sec) 0.7000000 now iterating at: 07:16:07 rms-change max change #iterations 3.094850 163.8426 at 10iterations 1.290058 65.56462 at 20iterations 0.5350648 21.45321 at 30iterations 0.2226981 8.362015 at 40iterations 9.2873700E-02 3.573794 at 50iterations 3.8551934E-02 1.502195 at 60iterations 1.6028002E-02 0.6166914 at 70iterations 6.6642179E-03 0.2861338 at 80iterations 2.7672411E-03 0.1104145 at 90iterations 1.1490745E-03 4.6008110E-02 at 100iterations 4.7918010E-04 1.7570615E-02 at 110iterations 1.9961031E-04 7.8969002E-03 at 120iterations finished qdiffx linear iterations at : 07:16:13 total time elapsed so far: 7.110000 # loops : 120 mean,max change (kT/e) : 1.9961031E-04 7.8969002E-03 energy calculations done at 7.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.290000 DelPhi exited at 07:16:13 7.294u 0.234s 0:07.83 96.0% 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 07:16:14 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 = 2537 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: 2.481759 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): -5.246000 41.45700 ymin,ymax (A): 37.65300 89.36400 zmin,zma (A): -2.670000 61.88100 x,y,z range (A): 46.70300 51.71100 64.55099 scale (grids/A): 2.481759 object centre (A): 18.10550 63.50850 29.60550 number of atom coordinates read : 2537 total number of charged atoms : 2391 net assigned charge : -9.499978 assigned positive charge : 379.0038 centred at (gu) : 94.43285 82.35475 87.53960 assigned negative charge : -388.5043 centred at (gu) : 95.24165 80.60886 87.24000 start vw surface at 0.1500000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 128444 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24904 grid for indexing accessible points = 1.400000 m= 56061 mr = 86798 m= 14907 mr = 43286 m= 2082 mr = 10733 m= 120 mr = 1223 m= 3 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 2895 time to turn everything in is 0.9700000 number of dielectric boundary points 59551 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 19117 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) : 1.654506 object centre at (A) : 18.10550 63.50850 29.60550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7797102 -2.3724150E-03 midg,1,midg; midg,igrid,midg -0.4751643 8.5227124E-02 1,midg,midg; igrid,midg,midg -4.6773821E-02 -0.2072303 gauss-seidel spectral radius is 0.9991288 estimated iterations to convergence 268 setup time was (sec) 1.320000 now iterating at: 07:16:15 rms-change max change #iterations 8.151265 350.5896 at 10iterations 4.551116 119.5045 at 20iterations 2.542482 87.28770 at 30iterations 1.414157 39.25096 at 40iterations 0.7813485 20.42381 at 50iterations 0.4317845 10.03174 at 60iterations 0.2379999 5.418004 at 70iterations 0.1309137 2.899426 at 80iterations 7.1985297E-02 1.531892 at 90iterations 3.9499342E-02 0.8713598 at 100iterations 2.1704562E-02 0.5138626 at 110iterations 1.1881246E-02 0.2705002 at 120iterations 6.5279538E-03 0.1708450 at 130iterations 3.5729138E-03 7.8096390E-02 at 140iterations 1.9531137E-03 4.7510147E-02 at 150iterations 1.0720902E-03 2.3761749E-02 at 160iterations 5.8642356E-04 1.5872955E-02 at 170iterations 3.2140731E-04 6.7234039E-03 at 180iterations finished qdiffx linear iterations at : 07:16:25 total time elapsed so far: 11.68000 # loops : 180 mean,max change (kT/e) : 3.2140731E-04 6.7234039E-03 energy calculations done at 11.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.85000 DelPhi exited at 07:16:26 11.854u 0.252s 0:12.39 97.6% 0+0k 0+0io 0pf+0w