Sun Oct 9 23:44:32 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 23:44:32 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2821 !!! WARNING: SEP 138 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: 0.5311926 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): -40.70400 26.31500 ymin,ymax (A): -26.86900 24.03200 zmin,zma (A): -7.750000 36.39200 x,y,z range (A): 67.01900 50.90100 44.14200 scale (grids/A): 0.5311926 object centre (A): -7.194501 -1.418500 14.32100 number of atom coordinates read : 2821 total number of charged atoms : 2677 net assigned charge : 4.525009 assigned positive charge : 432.5486 centred at (gu) : 89.73766 89.68464 89.45509 assigned negative charge : -428.0245 centred at (gu) : 89.79230 89.77581 89.41186 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5140 nv = 96 ne = 84 npr = 54137 no. pairs analyzed = 54137 no. exposed pairs = 3830 no. arc points = 27710 no. surface atoms = 1265 nbur = 1556 mkacc time = 9.9999994E-02 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 = 1.596000 m= 188 mr = 2409 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 2911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2826 ## 462 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6833 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2358421E-12 2.7100344E-10 midg,1,midg; midg,igrid,midg 5.2195936E-10 -1.6499765E-10 1,midg,midg; igrid,midg,midg 3.7586986E-10 -4.1245441E-11 gauss-seidel spectral radius is 0.9817350 estimated iterations to convergence 61 setup time was (sec) 0.3800000 now iterating at: 23:44:32 rms-change max change #iterations 6.2945127E-02 12.36245 at 10iterations 3.9092735E-03 0.7361242 at 20iterations 2.3656309E-04 3.9972305E-02 at 30iterations 1.4621664E-05 2.4795532E-03 at 40iterations 9.3810172E-07 1.7547607E-04 at 50iterations finished qdiffx linear iterations at : 23:44:35 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 9.3810172E-07 1.7547607E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 23:44:36 3.411u 0.192s 0:03.87 93.0% 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 23:44:36 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2821 !!! WARNING: SEP 138 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: 1.593578 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): -40.70400 26.31500 ymin,ymax (A): -26.86900 24.03200 zmin,zma (A): -7.750000 36.39200 x,y,z range (A): 67.01900 50.90100 44.14200 scale (grids/A): 1.593578 object centre (A): -7.194501 -1.418500 14.32100 number of atom coordinates read : 2821 total number of charged atoms : 2677 net assigned charge : 4.525009 assigned positive charge : 432.5486 centred at (gu) : 89.21236 89.05319 88.36467 assigned negative charge : -428.0245 centred at (gu) : 89.37654 89.32742 88.23531 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 57282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27710 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 15620 mr = 36496 m= 1318 mr = 10072 m= 36 mr = 561 m= 0 mr = 1 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 929 time to turn everything in is 0.2900000 number of dielectric boundary points 27126 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 392 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 20338 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) : 0.5311926 object centre at (A) : -7.194501 -1.418500 14.32100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3414056E-03 3.3158558E-05 midg,1,midg; midg,igrid,midg 6.7783268E-03 2.0619426E-03 1,midg,midg; igrid,midg,midg 1.2058345E-02 2.8354083E-03 gauss-seidel spectral radius is 0.9980740 estimated iterations to convergence 181 setup time was (sec) 0.5100000 now iterating at: 23:44:36 rms-change max change #iterations 3.044341 151.1067 at 10iterations 1.226481 55.39868 at 20iterations 0.4953003 19.69891 at 30iterations 0.2013902 8.489899 at 40iterations 8.1225693E-02 3.287507 at 50iterations 3.2973420E-02 1.346104 at 60iterations 1.3365739E-02 0.5310516 at 70iterations 5.4005976E-03 0.2033195 at 80iterations 2.1845233E-03 9.2099190E-02 at 90iterations 8.8601367E-04 3.5140514E-02 at 100iterations 3.5889138E-04 1.3787270E-02 at 110iterations 1.4559727E-04 5.8937073E-03 at 120iterations finished qdiffx linear iterations at : 23:44:43 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 1.4559727E-04 5.8937073E-03 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 23:44:44 7.685u 0.181s 0:08.13 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 23:44:44 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2821 !!! WARNING: SEP 138 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: 2.390367 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): -40.70400 26.31500 ymin,ymax (A): -26.86900 24.03200 zmin,zma (A): -7.750000 36.39200 x,y,z range (A): 67.01900 50.90100 44.14200 scale (grids/A): 2.390367 object centre (A): -7.194501 -1.418500 14.32100 number of atom coordinates read : 2821 total number of charged atoms : 2677 net assigned charge : 4.525009 assigned positive charge : 432.5486 centred at (gu) : 88.81848 88.57959 87.54688 assigned negative charge : -428.0245 centred at (gu) : 89.06472 88.99122 87.35303 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 133163 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27710 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 55760 mr = 90145 m= 14005 mr = 42411 m= 1957 mr = 10098 m= 86 mr = 1097 m= 0 mr = 20 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 3101 time to turn everything in is 0.6700000 number of dielectric boundary points 61200 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 21387 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) : 1.593578 object centre at (A) : -7.194501 -1.418500 14.32100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0966648E-02 -6.1378535E-04 midg,1,midg; midg,igrid,midg 0.1075797 6.3871317E-02 1,midg,midg; igrid,midg,midg 7.1160197E-02 -3.4218058E-02 gauss-seidel spectral radius is 0.9990953 estimated iterations to convergence 263 setup time was (sec) 0.9000000 now iterating at: 23:44:45 rms-change max change #iterations 7.966846 258.9041 at 10iterations 4.324616 131.0615 at 20iterations 2.343130 54.67644 at 30iterations 1.271035 27.81308 at 40iterations 0.6876197 19.64317 at 50iterations 0.3712972 8.212280 at 60iterations 0.2009364 4.872627 at 70iterations 0.1085714 2.378567 at 80iterations 5.8422141E-02 1.450663 at 90iterations 3.1560503E-02 0.6670914 at 100iterations 1.7028401E-02 0.4260492 at 110iterations 9.2445156E-03 0.2069244 at 120iterations 4.9625286E-03 0.1148038 at 130iterations 2.6779226E-03 6.2781811E-02 at 140iterations 1.4462582E-03 3.0639648E-02 at 150iterations 7.8316627E-04 1.7461300E-02 at 160iterations 4.2261023E-04 9.8032951E-03 at 170iterations 2.2800549E-04 5.2862167E-03 at 180iterations finished qdiffx linear iterations at : 23:44:56 total time elapsed so far: 11.94000 # loops : 180 mean,max change (kT/e) : 2.2800549E-04 5.2862167E-03 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.07000 DelPhi exited at 23:44:56 12.073u 0.209s 0:12.55 97.7% 0+0k 0+0io 0pf+0w