Sat Oct 8 17:55:38 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 17:55:39 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3279 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: 0.5518610 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): -0.4779999 64.03100 ymin,ymax (A): 14.68200 76.55600 zmin,zma (A): -13.30100 34.83000 x,y,z range (A): 64.50900 61.87400 48.13100 scale (grids/A): 0.5518610 object centre (A): 31.77650 45.61900 10.76450 number of atom coordinates read : 3279 total number of charged atoms : 3138 net assigned charge : 2.000005 assigned positive charge : 492.2437 centred at (gu) : 89.74986 86.74514 89.17159 assigned negative charge : -490.2450 centred at (gu) : 89.87299 86.78711 89.16351 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6566 nv = 96 ne = 84 npr = 66562 no. pairs analyzed = 66562 no. exposed pairs = 3997 no. arc points = 27419 no. surface atoms = 1364 nbur = 1915 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 = 1.568000 m= 273 mr = 3599 m= 1 mr = 8 m= 0 mr = 0 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 3233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2867 ## 378 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8511 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.9479562E-11 1.7319265E-10 midg,1,midg; midg,igrid,midg 1.1618644E-09 -1.0571646E-10 1,midg,midg; igrid,midg,midg 1.3061858E-09 -9.2422692E-10 gauss-seidel spectral radius is 0.9830872 estimated iterations to convergence 63 setup time was (sec) 0.5800000 now iterating at: 17:55:39 rms-change max change #iterations 8.0970787E-02 13.40184 at 10iterations 5.5991346E-03 0.8615189 at 20iterations 4.1512976E-04 6.2578201E-02 at 30iterations 5.1729909E-05 1.0367870E-02 at 40iterations 1.1661636E-05 2.4709702E-03 at 50iterations finished qdiffx linear iterations at : 17:55:42 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.1661636E-05 2.4709702E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 17:55:42 3.375u 0.208s 0:03.89 91.7% 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 17:55:42 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3279 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: 1.655583 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): -0.4779999 64.03100 ymin,ymax (A): 14.68200 76.55600 zmin,zma (A): -13.30100 34.83000 x,y,z range (A): 64.50900 61.87400 48.13100 scale (grids/A): 1.655583 object centre (A): 31.77650 45.61900 10.76450 number of atom coordinates read : 3279 total number of charged atoms : 3138 net assigned charge : 2.000005 assigned positive charge : 492.2437 centred at (gu) : 89.24889 80.23467 87.51404 assigned negative charge : -490.2450 centred at (gu) : 89.61825 80.36082 87.48988 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73107 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27419 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23443 mr = 51439 m= 2600 mr = 16483 m= 52 mr = 1302 m= 0 mr = 5 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 57 time to turn everything in is 0.5200000 number of dielectric boundary points 29973 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 319 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 24107 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) : 0.5518610 object centre at (A) : 31.77650 45.61900 10.76450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1862171E-03 1.2158575E-03 midg,1,midg; midg,igrid,midg -1.6353263E-02 -1.1242480E-02 1,midg,midg; igrid,midg,midg 3.3671647E-02 -6.0769194E-03 gauss-seidel spectral radius is 0.9982533 estimated iterations to convergence 190 setup time was (sec) 0.8100000 now iterating at: 17:55:43 rms-change max change #iterations 3.612706 172.6010 at 10iterations 1.534243 56.78498 at 20iterations 0.6518220 26.91244 at 30iterations 0.2764608 9.573204 at 40iterations 0.1170349 4.085704 at 50iterations 4.9646430E-02 1.545092 at 60iterations 2.1156631E-02 0.7082132 at 70iterations 9.0038516E-03 0.2940331 at 80iterations 3.8302285E-03 0.1326694 at 90iterations 1.6324684E-03 5.2484512E-02 at 100iterations 6.9728721E-04 2.5680542E-02 at 110iterations 3.0245507E-04 9.7045898E-03 at 120iterations finished qdiffx linear iterations at : 17:55:50 total time elapsed so far: 7.270000 # loops : 120 mean,max change (kT/e) : 3.0245507E-04 9.7045898E-03 energy calculations done at 7.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.450000 DelPhi exited at 17:55:50 7.451u 0.229s 0:07.95 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 Sat Oct 8 2011 at 17:55:50 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3279 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.483375 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): -0.4779999 64.03100 ymin,ymax (A): 14.68200 76.55600 zmin,zma (A): -13.30100 34.83000 x,y,z range (A): 64.50900 61.87400 48.13100 scale (grids/A): 2.483375 object centre (A): 31.77650 45.61900 10.76450 number of atom coordinates read : 3279 total number of charged atoms : 3138 net assigned charge : 2.000005 assigned positive charge : 492.2437 centred at (gu) : 88.87302 75.35186 86.27112 assigned negative charge : -490.2450 centred at (gu) : 89.42749 75.54119 86.23471 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 169915 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27419 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 81136 mr = 125337 m= 23410 mr = 65249 m= 4033 mr = 17835 m= 281 mr = 2687 m= 3 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 186 time to turn everything in is 1.240000 number of dielectric boundary points 67549 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 25087 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) : 1.655583 object centre at (A) : 31.77650 45.61900 10.76450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2735563E-02 9.3902899E-03 midg,1,midg; midg,igrid,midg -0.4287521 -0.1801575 1,midg,midg; igrid,midg,midg 0.4244186 -9.7443290E-02 gauss-seidel spectral radius is 0.9991575 estimated iterations to convergence 272 setup time was (sec) 1.560000 now iterating at: 17:55:52 rms-change max change #iterations 9.214337 343.5986 at 10iterations 5.192228 110.2182 at 20iterations 2.923289 60.46143 at 30iterations 1.635479 34.48728 at 40iterations 0.9120697 18.78132 at 50iterations 0.5081406 10.33361 at 60iterations 0.2827749 5.878670 at 70iterations 0.1568827 3.258133 at 80iterations 8.6869903E-02 1.646152 at 90iterations 4.8157908E-02 0.9469490 at 100iterations 2.6702102E-02 0.5184178 at 110iterations 1.4806534E-02 0.3107882 at 120iterations 8.2197208E-03 0.1598437 at 130iterations 4.5568245E-03 9.4135284E-02 at 140iterations 2.5303978E-03 4.5139313E-02 at 150iterations 1.4061208E-03 2.6077271E-02 at 160iterations 7.8470464E-04 1.4890671E-02 at 170iterations 4.4037538E-04 9.2887878E-03 at 180iterations finished qdiffx linear iterations at : 17:56:03 total time elapsed so far: 11.88000 # loops : 180 mean,max change (kT/e) : 4.4037538E-04 9.2887878E-03 energy calculations done at 11.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.05000 DelPhi exited at 17:56:03 12.052u 0.243s 0:12.57 97.7% 0+0k 0+0io 0pf+0w