Sun Oct 9 21:23:24 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 21:23:24 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2983 !!! WARNING: SEP 139 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6337452 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): -9.059999 44.21900 ymin,ymax (A): -27.57800 28.59600 zmin,zma (A): -2.387000 51.92500 x,y,z range (A): 53.27900 56.17400 54.31200 scale (grids/A): 0.6337452 object centre (A): 17.57950 0.5089998 24.76900 number of atom coordinates read : 2983 total number of charged atoms : 2833 net assigned charge : 6.525014 assigned positive charge : 454.7771 centred at (gu) : 91.16886 91.02741 90.11963 assigned negative charge : -448.2531 centred at (gu) : 91.17354 90.92137 90.07174 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7944 nv = 96 ne = 84 npr = 58868 no. pairs analyzed = 58868 no. exposed pairs = 3909 no. arc points = 28238 no. surface atoms = 1308 nbur = 1675 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 429 mr = 4022 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.2100000 number of dielectric boundary points 4297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2842 ## 299 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9705 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2745099E-09 1.3506860E-08 midg,1,midg; midg,igrid,midg -3.4138337E-09 2.4538167E-08 1,midg,midg; igrid,midg,midg 6.5146950E-09 9.2460191E-09 gauss-seidel spectral radius is 0.9871458 estimated iterations to convergence 72 setup time was (sec) 0.3900000 now iterating at: 21:23:24 rms-change max change #iterations 0.1471261 19.97275 at 10iterations 1.4244070E-02 1.907922 at 20iterations 1.3886694E-03 0.2046738 at 30iterations 1.3669270E-04 1.9914627E-02 at 40iterations 1.4246912E-05 1.8692017E-03 at 50iterations finished qdiffx linear iterations at : 21:23:27 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.4246912E-05 1.8692017E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 21:23:27 3.362u 0.175s 0:03.80 92.8% 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 21:23:28 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2983 !!! WARNING: SEP 139 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.901236 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): -9.059999 44.21900 ymin,ymax (A): -27.57800 28.59600 zmin,zma (A): -2.387000 51.92500 x,y,z range (A): 53.27900 56.17400 54.31200 scale (grids/A): 1.901236 object centre (A): 17.57950 0.5089998 24.76900 number of atom coordinates read : 2983 total number of charged atoms : 2833 net assigned charge : 6.525014 assigned positive charge : 454.7771 centred at (gu) : 93.50605 93.08183 90.35806 assigned negative charge : -448.2531 centred at (gu) : 93.52015 92.76374 90.21470 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28238 grid for indexing accessible points = 1.400000 m= 28933 mr = 56124 m= 4476 mr = 20444 m= 273 mr = 2669 m= 2 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1911 time to turn everything in is 0.4100000 number of dielectric boundary points 39709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 188 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 22245 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) : 0.6337452 object centre at (A) : 17.57950 0.5089998 24.76900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4774496E-02 1.9652776E-03 midg,1,midg; midg,igrid,midg 1.6164564E-02 1.7498294E-02 1,midg,midg; igrid,midg,midg 2.4758410E-03 -6.9923433E-03 gauss-seidel spectral radius is 0.9986829 estimated iterations to convergence 218 setup time was (sec) 0.6300000 now iterating at: 21:23:28 rms-change max change #iterations 4.555446 167.1403 at 10iterations 2.152911 75.64350 at 20iterations 1.017327 37.39507 at 30iterations 0.4805157 14.86077 at 40iterations 0.2277623 6.694957 at 50iterations 0.1077601 3.476980 at 60iterations 5.0958619E-02 1.868011 at 70iterations 2.4165560E-02 0.7310350 at 80iterations 1.1465870E-02 0.3545094 at 90iterations 5.4469109E-03 0.1647053 at 100iterations 2.5673422E-03 7.8117371E-02 at 110iterations 1.2199425E-03 3.6572456E-02 at 120iterations finished qdiffx linear iterations at : 21:23:35 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 1.2199425E-03 3.6572456E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 21:23:36 7.805u 0.185s 0:08.26 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 Sun Oct 9 2011 at 21:23:36 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2983 !!! WARNING: SEP 139 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.851853 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): -9.059999 44.21900 ymin,ymax (A): -27.57800 28.59600 zmin,zma (A): -2.387000 51.92500 x,y,z range (A): 53.27900 56.17400 54.31200 scale (grids/A): 2.851853 object centre (A): 17.57950 0.5089998 24.76900 number of atom coordinates read : 2983 total number of charged atoms : 2833 net assigned charge : 6.525014 assigned positive charge : 454.7771 centred at (gu) : 95.25886 94.62238 90.53701 assigned negative charge : -448.2531 centred at (gu) : 95.28006 94.14557 90.32208 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 197485 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28238 grid for indexing accessible points = 1.400000 m= 93799 mr = 136791 m= 32669 mr = 74671 m= 7860 mr = 25373 m= 1238 mr = 5747 m= 77 mr = 868 m= 2 mr = 55 m= 0 mr = 2 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 6986 time to turn everything in is 1.060000 number of dielectric boundary points 89623 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 22663 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) : 1.901236 object centre at (A) : 17.57950 0.5089998 24.76900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1842145 -0.1226937 midg,1,midg; midg,igrid,midg 0.1414350 0.1599441 1,midg,midg; igrid,midg,midg 9.6921928E-02 -0.2953785 gauss-seidel spectral radius is 0.9992905 estimated iterations to convergence 296 setup time was (sec) 1.290000 now iterating at: 21:23:37 rms-change max change #iterations 10.89806 312.7513 at 10iterations 6.481714 140.2970 at 20iterations 3.842841 79.53671 at 30iterations 2.267796 46.76258 at 40iterations 1.328897 25.78833 at 50iterations 0.7789376 13.86421 at 60iterations 0.4551862 7.915872 at 70iterations 0.2656637 5.748575 at 80iterations 0.1550788 2.738200 at 90iterations 9.0208471E-02 1.626011 at 100iterations 5.2580781E-02 0.9707440 at 110iterations 3.0570185E-02 0.5709112 at 120iterations 1.7755097E-02 0.2958415 at 130iterations 1.0331100E-02 0.1831517 at 140iterations 6.0109589E-03 9.8976135E-02 at 150iterations 3.4876985E-03 5.8898926E-02 at 160iterations 2.0296315E-03 3.2899857E-02 at 170iterations 1.1818190E-03 1.9708872E-02 at 180iterations finished qdiffx linear iterations at : 21:23:49 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 1.1818190E-03 1.9708872E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 21:23:49 12.914u 0.213s 0:13.39 97.9% 0+0k 0+0io 0pf+0w