Sun Oct 9 21:21:51 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 21:21:51 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2854 !!! 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: 0.5843825 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 : 2706 net assigned charge : 6.525013 assigned positive charge : 433.9594 centred at (gu) : 90.27637 90.32725 90.68343 assigned negative charge : -427.4352 centred at (gu) : 90.34550 90.31089 90.82520 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 = 0.1100000 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 4.3528674E-09 -2.1721487E-09 midg,1,midg; midg,igrid,midg 1.2013872E-09 2.2534103E-09 1,midg,midg; igrid,midg,midg 3.1605600E-09 -1.8322559E-11 gauss-seidel spectral radius is 0.9848829 estimated iterations to convergence 67 setup time was (sec) 0.4100000 now iterating at: 21:21:52 rms-change max change #iterations 0.1006257 16.44678 at 10iterations 7.9808226E-03 1.273441 at 20iterations 6.3569407E-04 9.6370697E-02 at 30iterations 5.0951170E-05 7.8563690E-03 at 40iterations 4.2249435E-06 6.7901611E-04 at 50iterations finished qdiffx linear iterations at : 21:21:55 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 4.2249435E-06 6.7901611E-04 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 21:21:55 3.443u 0.178s 0:03.92 92.0% 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 21:21:55 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2854 !!! 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: 1.753148 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 : 2706 net assigned charge : 6.525013 assigned positive charge : 433.9594 centred at (gu) : 90.82856 90.98102 92.04942 assigned negative charge : -427.4352 centred at (gu) : 91.03619 90.93230 92.47557 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 = 0.1500000 no. cavity mid-points inaccessible to solvent = 423 time to turn everything in is 0.3500000 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 0.4300000 number of grid points assigned charge 21023 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 2.9375004E-02 -5.1555090E-04 midg,1,midg; midg,igrid,midg 4.7159372E-03 -8.2429248E-04 1,midg,midg; igrid,midg,midg -3.7708199E-03 1.2309617E-02 gauss-seidel spectral radius is 0.9984354 estimated iterations to convergence 201 setup time was (sec) 0.5700000 now iterating at: 21:21:56 rms-change max change #iterations 3.808568 177.6090 at 10iterations 1.675029 61.37917 at 20iterations 0.7407271 25.64118 at 30iterations 0.3279767 11.77859 at 40iterations 0.1457735 5.402056 at 50iterations 6.4544730E-02 2.285805 at 60iterations 2.8544182E-02 1.068707 at 70iterations 1.2631112E-02 0.4708443 at 80iterations 5.6106150E-03 0.1934414 at 90iterations 2.4788389E-03 8.1880569E-02 at 100iterations 1.1004253E-03 4.1232586E-02 at 110iterations 4.8956979E-04 1.6632080E-02 at 120iterations finished qdiffx linear iterations at : 21:22:03 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 4.8956979E-04 1.6632080E-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) 7.860000 DelPhi exited at 21:22:04 7.867u 0.207s 0:08.41 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 21:22:04 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2854 !!! 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: 2.629721 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 : 2706 net assigned charge : 6.525013 assigned positive charge : 433.9594 centred at (gu) : 91.24242 91.47133 93.07397 assigned negative charge : -427.4352 centred at (gu) : 91.55419 91.39838 93.71326 start vw surface at 9.0000004E-02 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 0.8300000 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 0.9200000 number of grid points assigned charge 21642 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 0.4343337 -0.2653596 midg,1,midg; midg,igrid,midg 0.1378655 -5.7073995E-02 1,midg,midg; igrid,midg,midg -0.1402526 0.1825001 gauss-seidel spectral radius is 0.9992204 estimated iterations to convergence 283 setup time was (sec) 1.070000 now iterating at: 21:22:05 rms-change max change #iterations 9.362940 266.0925 at 10iterations 5.383348 124.1888 at 20iterations 3.061320 72.38843 at 30iterations 1.743979 34.99916 at 40iterations 0.9884951 20.38968 at 50iterations 0.5605225 10.89082 at 60iterations 0.3173520 6.290686 at 70iterations 0.1791745 3.566936 at 80iterations 0.1013219 1.917709 at 90iterations 5.7261016E-02 1.182130 at 100iterations 3.2373153E-02 0.6531711 at 110iterations 1.8303163E-02 0.3633327 at 120iterations 1.0328921E-02 0.1862125 at 130iterations 5.8353068E-03 0.1191101 at 140iterations 3.2964388E-03 6.3925505E-02 at 150iterations 1.8614394E-03 3.7408829E-02 at 160iterations 1.0523107E-03 2.0206451E-02 at 170iterations 5.9551117E-04 1.2073517E-02 at 180iterations finished qdiffx linear iterations at : 21:22:17 total time elapsed so far: 12.57000 # loops : 180 mean,max change (kT/e) : 5.9551117E-04 1.2073517E-02 energy calculations done at 12.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 21:22:17 12.709u 0.207s 0:13.20 97.7% 0+0k 0+0io 0pf+0w