Sat Oct 8 17:49:14 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 8 2011 at 17:49:14 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3390 !!! WARNING: SEP 310 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5210620 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): 40.89200 109.2140 ymin,ymax (A): 10.80800 61.04600 zmin,zma (A): 2.909000 51.03000 x,y,z range (A): 68.32201 50.23800 48.12100 scale (grids/A): 0.5210620 object centre (A): 75.05300 35.92700 26.96950 number of atom coordinates read : 3390 total number of charged atoms : 3243 net assigned charge : -4.474995 assigned positive charge : 509.5374 centred at (gu) : 90.22613 88.19664 90.24276 assigned negative charge : -514.0138 centred at (gu) : 90.21395 88.12784 90.24010 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6038 nv = 96 ne = 84 npr = 67725 no. pairs analyzed = 67725 no. exposed pairs = 4216 no. arc points = 28941 no. surface atoms = 1416 nbur = 1974 mkacc time = 0.1500000 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= 238 mr = 3245 m= 0 mr = 4 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3027 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2912 ## 402 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7900 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.7554728E-11 -9.3914300E-11 midg,1,midg; midg,igrid,midg -4.7478177E-10 6.1593959E-11 1,midg,midg; igrid,midg,midg -1.2387816E-10 -6.4455476E-11 gauss-seidel spectral radius is 0.9810600 estimated iterations to convergence 60 setup time was (sec) 0.5700000 now iterating at: 17:49:14 rms-change max change #iterations 6.2826209E-02 10.29488 at 10iterations 3.7511261E-03 0.6129589 at 20iterations 2.8557717E-04 5.6066513E-02 at 30iterations 4.7499110E-05 1.1075020E-02 at 40iterations 1.1763083E-05 2.7980804E-03 at 50iterations finished qdiffx linear iterations at : 17:49:17 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.1763083E-05 2.7980804E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 17:49:18 3.437u 0.199s 0:03.91 92.5% 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 Sat Oct 8 2011 at 17:49:18 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3390 !!! WARNING: SEP 310 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.563186 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): 40.89200 109.2140 ymin,ymax (A): 10.80800 61.04600 zmin,zma (A): 2.909000 51.03000 x,y,z range (A): 68.32201 50.23800 48.12100 scale (grids/A): 1.563186 object centre (A): 75.05300 35.92700 26.96950 number of atom coordinates read : 3390 total number of charged atoms : 3243 net assigned charge : -4.474995 assigned positive charge : 509.5374 centred at (gu) : 90.67766 84.58910 90.72749 assigned negative charge : -514.0138 centred at (gu) : 90.64159 84.38319 90.71983 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 67656 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28941 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20700 mr = 47177 m= 1987 mr = 14371 m= 42 mr = 916 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 442 time to turn everything in is 0.4900000 number of dielectric boundary points 27921 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 404 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 24561 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) : 0.5210620 object centre at (A) : 75.05300 35.92700 26.96950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1659949E-03 -2.3867970E-03 midg,1,midg; midg,igrid,midg -6.7912084E-03 9.9264528E-04 1,midg,midg; igrid,midg,midg 1.2040677E-02 -5.1129223E-03 gauss-seidel spectral radius is 0.9980482 estimated iterations to convergence 180 setup time was (sec) 0.8000000 now iterating at: 17:49:19 rms-change max change #iterations 3.265679 131.9915 at 10iterations 1.322724 51.18326 at 20iterations 0.5363617 19.99825 at 30iterations 0.2165239 9.232629 at 40iterations 8.7525927E-02 3.438950 at 50iterations 3.5516098E-02 1.227180 at 60iterations 1.4349469E-02 0.5525824 at 70iterations 5.8281776E-03 0.2230072 at 80iterations 2.3678811E-03 8.6855888E-02 at 90iterations 9.6517778E-04 3.9306641E-02 at 100iterations 4.0090599E-04 1.3977051E-02 at 110iterations 1.7151974E-04 6.3152313E-03 at 120iterations finished qdiffx linear iterations at : 17:49:25 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 1.7151974E-04 6.3152313E-03 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 17:49:26 7.846u 0.227s 0:08.34 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 Sat Oct 8 2011 at 17:49:26 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3390 !!! WARNING: SEP 310 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.344779 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): 40.89200 109.2140 ymin,ymax (A): 10.80800 61.04600 zmin,zma (A): 2.909000 51.03000 x,y,z range (A): 68.32201 50.23800 48.12100 scale (grids/A): 2.344779 object centre (A): 75.05300 35.92700 26.96950 number of atom coordinates read : 3390 total number of charged atoms : 3243 net assigned charge : -4.474995 assigned positive charge : 509.5374 centred at (gu) : 91.01614 81.88340 91.09089 assigned negative charge : -514.0138 centred at (gu) : 90.96203 81.57473 91.07967 start vw surface at 0.1700000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 157535 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28941 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 73347 mr = 115519 m= 19867 mr = 58613 m= 2947 mr = 14858 m= 168 mr = 1821 m= 3 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 1504 time to turn everything in is 1.190000 number of dielectric boundary points 63005 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 25884 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) : 1.563186 object centre at (A) : 75.05300 35.92700 26.96950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1059718E-02 -2.7733460E-02 midg,1,midg; midg,igrid,midg -0.1002401 3.2435447E-02 1,midg,midg; igrid,midg,midg 0.3951514 -0.1509662 gauss-seidel spectral radius is 0.9990977 estimated iterations to convergence 263 setup time was (sec) 1.500000 now iterating at: 17:49:28 rms-change max change #iterations 8.604701 263.9116 at 10iterations 4.744160 109.5670 at 20iterations 2.598370 67.28934 at 30iterations 1.422730 30.68188 at 40iterations 0.7771879 16.40042 at 50iterations 0.4228738 10.31125 at 60iterations 0.2296584 4.974308 at 70iterations 0.1246076 2.421000 at 80iterations 6.7808680E-02 1.524253 at 90iterations 3.6853395E-02 0.7121391 at 100iterations 1.9946976E-02 0.4627955 at 110iterations 1.0843527E-02 0.2186127 at 120iterations 5.8747195E-03 0.1352997 at 130iterations 3.1811427E-03 6.9292545E-02 at 140iterations 1.7292035E-03 3.9150238E-02 at 150iterations 9.4112311E-04 1.8447876E-02 at 160iterations 5.1303481E-04 9.7885132E-03 at 170iterations 2.8114955E-04 5.8670044E-03 at 180iterations finished qdiffx linear iterations at : 17:49:39 total time elapsed so far: 12.52000 # loops : 180 mean,max change (kT/e) : 2.8114955E-04 5.8670044E-03 energy calculations done at 12.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 17:49:39 12.700u 0.222s 0:13.19 97.9% 0+0k 0+0io 0pf+0w