Sun Oct 9 19:03:19 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 Sun Oct 9 2011 at 19:03:19 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5368 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5491539 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): 3.253000 68.08000 ymin,ymax (A): -8.956000 53.32500 zmin,zma (A): -1.005000 63.63200 x,y,z range (A): 64.82700 62.28100 64.63700 scale (grids/A): 0.5491539 object centre (A): 35.66650 22.18450 31.31350 number of atom coordinates read : 5368 total number of charged atoms : 5215 net assigned charge : 1.649049 assigned positive charge : 827.4138 centred at (gu) : 88.22070 89.13112 89.21754 assigned negative charge : -825.7712 centred at (gu) : 88.12780 89.13889 89.17519 start vw surface at 0.2400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 10557 nv = 96 ne = 84 npr = 109647 no. pairs analyzed = 109647 no. exposed pairs = 6127 no. arc points = 41903 no. surface atoms = 2094 nbur = 3274 mkacc time = 0.2600000 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 = 1.568000 m= 446 mr = 6112 m= 1 mr = 25 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 0.5500000 number of dielectric boundary points 4867 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4285 ## 482 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 13874 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3974075E-10 5.9929445E-10 midg,1,midg; midg,igrid,midg 3.1330299E-10 3.1713080E-11 1,midg,midg; igrid,midg,midg -1.8126853E-09 9.1141206E-10 gauss-seidel spectral radius is 0.9830720 estimated iterations to convergence 63 setup time was (sec) 0.7800000 now iterating at: 19:03:20 rms-change max change #iterations 0.1075982 12.69455 at 10iterations 9.6338121E-03 1.258202 at 20iterations 2.6674082E-03 0.2990036 at 30iterations 1.1888390E-03 0.1392994 at 40iterations 5.5316160E-04 6.9892406E-02 at 50iterations finished qdiffx linear iterations at : 19:03:23 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 5.5316160E-04 6.9892406E-02 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 19:03:23 3.594u 0.140s 0:04.04 92.3% 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 19:03:23 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5368 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.647462 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): 3.253000 68.08000 ymin,ymax (A): -8.956000 53.32500 zmin,zma (A): -1.005000 63.63200 x,y,z range (A): 64.82700 62.28100 64.63700 scale (grids/A): 1.647462 object centre (A): 35.66650 22.18450 31.31350 number of atom coordinates read : 5368 total number of charged atoms : 5215 net assigned charge : 1.649049 assigned positive charge : 827.4138 centred at (gu) : 84.66064 87.39183 87.65089 assigned negative charge : -825.7712 centred at (gu) : 84.38316 87.41658 87.52542 start vw surface at 0.2300000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 117711 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41903 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 40363 mr = 85987 m= 4675 mr = 29258 m= 136 mr = 2546 m= 0 mr = 17 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 205 time to turn everything in is 0.8500000 number of dielectric boundary points 45077 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 426 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 40006 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) : 0.5491539 object centre at (A) : 35.66650 22.18450 31.31350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5425019E-02 1.7737044E-02 midg,1,midg; midg,igrid,midg 1.7663673E-02 8.1227906E-03 1,midg,midg; igrid,midg,midg -1.7826751E-02 6.2378538E-03 gauss-seidel spectral radius is 0.9984282 estimated iterations to convergence 200 setup time was (sec) 1.150000 now iterating at: 19:03:24 rms-change max change #iterations 4.926771 171.3747 at 10iterations 2.179812 75.50697 at 20iterations 0.9698061 25.57217 at 30iterations 0.4302323 11.59423 at 40iterations 0.1911962 6.355947 at 50iterations 8.5476160E-02 2.303703 at 60iterations 3.8534161E-02 1.030758 at 70iterations 1.7689962E-02 0.4973946 at 80iterations 8.5720960E-03 0.2486839 at 90iterations 4.5998460E-03 0.1378326 at 100iterations 2.8091320E-03 7.8826904E-02 at 110iterations 1.9293912E-03 4.9322605E-02 at 120iterations finished qdiffx linear iterations at : 19:03:31 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 1.9293912E-03 4.9322605E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 19:03:32 7.933u 0.170s 0:08.40 96.4% 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 Sun Oct 9 2011 at 19:03:32 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5368 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.471192 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): 3.253000 68.08000 ymin,ymax (A): -8.956000 53.32500 zmin,zma (A): -1.005000 63.63200 x,y,z range (A): 64.82700 62.28100 64.63700 scale (grids/A): 2.471192 object centre (A): 35.66650 22.18450 31.31350 number of atom coordinates read : 5368 total number of charged atoms : 5215 net assigned charge : 1.649049 assigned positive charge : 827.4138 centred at (gu) : 81.99061 86.08735 86.47588 assigned negative charge : -825.7712 centred at (gu) : 81.57477 86.12485 86.28806 start vw surface at 0.2300000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 273500 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41903 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 137422 mr = 208748 m= 42634 mr = 112590 m= 7588 mr = 33075 m= 610 mr = 5239 m= 19 mr = 325 m= 0 mr = 0 time to grow re-entrant surface = 1.280000 no. cavity mid-points inaccessible to solvent = 684 time to turn everything in is 2.110000 number of dielectric boundary points 101796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 41682 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) : 1.647462 object centre at (A) : 35.66650 22.18450 31.31350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4575125 0.4087969 midg,1,midg; midg,igrid,midg 0.1846847 3.2128089E-03 1,midg,midg; igrid,midg,midg -0.4696006 6.5505043E-02 gauss-seidel spectral radius is 0.9992558 estimated iterations to convergence 289 setup time was (sec) 2.420000 now iterating at: 19:03:34 rms-change max change #iterations 12.47785 414.8125 at 10iterations 7.340342 156.7152 at 20iterations 4.293052 80.82191 at 30iterations 2.503192 41.24329 at 40iterations 1.454477 23.38017 at 50iterations 0.8432692 13.32799 at 60iterations 0.4884068 8.214401 at 70iterations 0.2821118 4.465668 at 80iterations 0.1627685 2.536980 at 90iterations 9.3996860E-02 1.601210 at 100iterations 5.4295663E-02 0.9629288 at 110iterations 3.1420827E-02 0.5525055 at 120iterations 1.8332019E-02 0.2875671 at 130iterations 1.0849699E-02 0.2068367 at 140iterations 6.5887407E-03 0.1045914 at 150iterations 4.1769175E-03 7.4256897E-02 at 160iterations 2.8177770E-03 4.8899651E-02 at 170iterations 2.0453641E-03 3.2976151E-02 at 180iterations finished qdiffx linear iterations at : 19:03:45 total time elapsed so far: 13.11000 # loops : 180 mean,max change (kT/e) : 2.0453641E-03 3.2976151E-02 energy calculations done at 13.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.31000 DelPhi exited at 19:03:45 13.311u 0.175s 0:13.76 97.9% 0+0k 0+0io 0pf+0w