Sun Oct 9 21:21:25 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 21:21:26 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2854 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: 0.5843825 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): 42.53500 97.57401 ymin,ymax (A): 19.69600 72.18700 zmin,zma (A): 10.81600 71.73500 x,y,z range (A): 55.03901 52.49100 60.91900 scale (grids/A): 0.5843825 object centre (A): 70.05450 45.94150 41.27550 number of atom coordinates read : 2854 total number of charged atoms : 2708 net assigned charge : 7.000019 assigned positive charge : 432.8393 centred at (gu) : 90.26903 90.32997 90.68003 assigned negative charge : -425.8403 centred at (gu) : 90.33267 90.31139 90.82000 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6346 nv = 96 ne = 84 npr = 55717 no. pairs analyzed = 55717 no. exposed pairs = 3597 no. arc points = 26455 no. surface atoms = 1222 nbur = 1632 mkacc time = 9.0000004E-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 = 1.484000 m= 278 mr = 3180 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2782 ## 350 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8224 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4118926E-09 -1.9628610E-09 midg,1,midg; midg,igrid,midg 1.2623698E-09 2.4400801E-09 1,midg,midg; igrid,midg,midg 3.1488501E-09 2.5996510E-10 gauss-seidel spectral radius is 0.9848829 estimated iterations to convergence 67 setup time was (sec) 0.4000000 now iterating at: 21:21:26 rms-change max change #iterations 9.9754117E-02 16.44666 at 10iterations 7.9056956E-03 1.256445 at 20iterations 6.3144293E-04 9.7707748E-02 at 30iterations 5.0641876E-05 7.7881813E-03 at 40iterations 4.2335951E-06 6.7043304E-04 at 50iterations finished qdiffx linear iterations at : 21:21:29 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 4.2335951E-06 6.7043304E-04 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 21:21:30 3.458u 0.177s 0:03.96 91.4% 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 21:21:30 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 = 2854 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: 1.753148 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): 42.53500 97.57401 ymin,ymax (A): 19.69600 72.18700 zmin,zma (A): 10.81600 71.73500 x,y,z range (A): 55.03901 52.49100 60.91900 scale (grids/A): 1.753148 object centre (A): 70.05450 45.94150 41.27550 number of atom coordinates read : 2854 total number of charged atoms : 2708 net assigned charge : 7.000019 assigned positive charge : 432.8393 centred at (gu) : 90.80650 90.98915 92.03922 assigned negative charge : -425.8403 centred at (gu) : 90.99773 90.93378 92.45999 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 69739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26455 grid for indexing accessible points = 1.400000 m= 20862 mr = 45714 m= 2461 mr = 14173 m= 102 mr = 1322 m= 0 mr = 23 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 423 time to turn everything in is 0.3400000 number of dielectric boundary points 31932 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 298 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 21037 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) : 0.5843825 object centre at (A) : 70.05450 45.94150 41.27550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9503619E-02 3.8848280E-05 midg,1,midg; midg,igrid,midg 4.9262717E-03 -3.0822583E-04 1,midg,midg; igrid,midg,midg -3.7249299E-03 1.3895622E-02 gauss-seidel spectral radius is 0.9984354 estimated iterations to convergence 201 setup time was (sec) 0.5600000 now iterating at: 21:21:30 rms-change max change #iterations 3.785372 177.6090 at 10iterations 1.665241 61.37912 at 20iterations 0.7359579 25.83413 at 30iterations 0.3257970 11.78009 at 40iterations 0.1448366 5.489897 at 50iterations 6.4132974E-02 2.287090 at 60iterations 2.8362865E-02 1.035596 at 70iterations 1.2549741E-02 0.4711742 at 80iterations 5.5747000E-03 0.1907692 at 90iterations 2.4628351E-03 8.0837250E-02 at 100iterations 1.0931818E-03 4.0781498E-02 at 110iterations 4.8635760E-04 1.6197205E-02 at 120iterations finished qdiffx linear iterations at : 21:21:37 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 4.8635760E-04 1.6197205E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 21:21:38 7.903u 0.196s 0:08.44 95.8% 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 21:21:38 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 = 2854 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: 2.629721 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): 42.53500 97.57401 ymin,ymax (A): 19.69600 72.18700 zmin,zma (A): 10.81600 71.73500 x,y,z range (A): 55.03901 52.49100 60.91900 scale (grids/A): 2.629721 object centre (A): 70.05450 45.94150 41.27550 number of atom coordinates read : 2854 total number of charged atoms : 2708 net assigned charge : 7.000019 assigned positive charge : 432.8393 centred at (gu) : 91.20929 91.48350 93.05865 assigned negative charge : -425.8403 centred at (gu) : 91.49651 91.40058 93.68991 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 161896 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26455 grid for indexing accessible points = 1.400000 m= 71485 mr = 111935 m= 21004 mr = 56239 m= 4107 mr = 15590 m= 435 mr = 2824 m= 17 mr = 258 m= 0 mr = 9 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 1425 time to turn everything in is 0.8400000 number of dielectric boundary points 72089 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 21658 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) : 1.753148 object centre at (A) : 70.05450 45.94150 41.27550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4358782 -0.2590860 midg,1,midg; midg,igrid,midg 0.1403246 -5.1191937E-02 1,midg,midg; igrid,midg,midg -0.1397458 0.2033036 gauss-seidel spectral radius is 0.9992204 estimated iterations to convergence 283 setup time was (sec) 1.090000 now iterating at: 21:21:39 rms-change max change #iterations 9.318376 266.0925 at 10iterations 5.357763 124.1895 at 20iterations 3.047313 71.73597 at 30iterations 1.735555 34.99903 at 40iterations 0.9839331 20.43621 at 50iterations 0.5579827 10.72948 at 60iterations 0.3159210 6.291079 at 70iterations 0.1783545 3.524092 at 80iterations 0.1008544 1.962914 at 90iterations 5.7003275E-02 1.183064 at 100iterations 3.2228727E-02 0.6499801 at 110iterations 1.8226204E-02 0.3654861 at 120iterations 1.0282849E-02 0.1851349 at 130iterations 5.8106016E-03 0.1191788 at 140iterations 3.2819833E-03 6.3354492E-02 at 150iterations 1.8532863E-03 3.5999298E-02 at 160iterations 1.0479038E-03 1.9683838E-02 at 170iterations 5.9297326E-04 1.1562347E-02 at 180iterations finished qdiffx linear iterations at : 21:21:51 total time elapsed so far: 12.47000 # loops : 180 mean,max change (kT/e) : 5.9297326E-04 1.1562347E-02 energy calculations done at 12.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.61000 DelPhi exited at 21:21:51 12.611u 0.197s 0:13.16 97.2% 0+0k 0+0io 0pf+0w