Tue Nov 22 14:16:01 PST 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 Tue Nov 22 2011 at 14:16:05 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6431100 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): -5.373000 36.60400 ymin,ymax (A): -3.638000 48.58200 zmin,zma (A): -24.15200 31.20400 x,y,z range (A): 41.97700 52.22000 55.35600 scale (grids/A): 0.6431100 object centre (A): 15.61550 22.47200 3.526000 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 290.3020 centred at (gu) : 90.15456 92.77772 90.12725 assigned negative charge : -285.3022 centred at (gu) : 90.24186 92.86182 90.05900 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5751 nv = 96 ne = 84 npr = 39233 no. pairs analyzed = 39233 no. exposed pairs = 2482 no. arc points = 17729 no. surface atoms = 846 nbur = 1120 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 331 mr = 3221 m= 2 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.1600000 number of dielectric boundary points 2813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1734 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6511 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7536809E-09 1.4800296E-08 midg,1,midg; midg,igrid,midg 8.8976559E-09 6.5755602E-11 1,midg,midg; igrid,midg,midg 1.5620552E-08 -1.4353251E-11 gauss-seidel spectral radius is 0.9874219 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 14:16:08 rms-change max change #iterations 0.1255500 18.33609 at 10iterations 1.2616171E-02 1.858490 at 20iterations 1.2285048E-03 0.1868057 at 30iterations 1.2515442E-04 1.9382477E-02 at 40iterations 1.2550206E-05 1.9348264E-03 at 50iterations finished qdiffx linear iterations at : 14:16:18 total time elapsed so far: 3.670000 # loops : 50 mean,max change (kT/e) : 1.2550206E-05 1.9348264E-03 energy calculations done at 3.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.800000 DelPhi exited at 14:16:19 3.799u 0.209s 0:15.20 26.2% 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 Tue Nov 22 2011 at 14:16:25 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.929330 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): -5.373000 36.60400 ymin,ymax (A): -3.638000 48.58200 zmin,zma (A): -24.15200 31.20400 x,y,z range (A): 41.97700 52.22000 55.35600 scale (grids/A): 1.929330 object centre (A): 15.61550 22.47200 3.526000 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 290.3020 centred at (gu) : 90.46368 98.33296 90.38169 assigned negative charge : -285.3022 centred at (gu) : 90.72576 98.58549 90.17710 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 60630 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17729 grid for indexing accessible points = 1.400000 m= 24398 mr = 41486 m= 4289 mr = 19175 m= 254 mr = 2917 m= 2 mr = 109 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 291 time to turn everything in is 0.3200000 number of dielectric boundary points 25886 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 99 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 14455 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) : 0.6431100 object centre at (A) : 15.61550 22.47200 3.526000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2060388E-02 1.1436005E-02 midg,1,midg; midg,igrid,midg 3.0887064E-02 1.7139985E-03 1,midg,midg; igrid,midg,midg 8.6661829E-03 9.0483800E-03 gauss-seidel spectral radius is 0.9985979 estimated iterations to convergence 212 setup time was (sec) 0.5500000 now iterating at: 14:16:29 rms-change max change #iterations 3.665009 153.7669 at 10iterations 1.697195 62.01790 at 20iterations 0.7906834 28.48639 at 30iterations 0.3662804 12.64672 at 40iterations 0.1692591 5.685839 at 50iterations 7.8457445E-02 2.681247 at 60iterations 3.6239717E-02 1.410812 at 70iterations 1.6759723E-02 0.5547237 at 80iterations 7.8046406E-03 0.2753494 at 90iterations 3.6089045E-03 0.1177669 at 100iterations 1.6753691E-03 5.4865837E-02 at 110iterations 7.7668985E-04 3.1017303E-02 at 120iterations finished qdiffx linear iterations at : 14:16:53 total time elapsed so far: 8.440000 # loops : 120 mean,max change (kT/e) : 7.7668985E-04 3.1017303E-02 energy calculations done at 8.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.580000 DelPhi exited at 14:16:55 8.578u 0.254s 0:30.60 28.8% 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 Tue Nov 22 2011 at 14:16:57 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.893995 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): -5.373000 36.60400 ymin,ymax (A): -3.638000 48.58200 zmin,zma (A): -24.15200 31.20400 x,y,z range (A): 41.97700 52.22000 55.35600 scale (grids/A): 2.893995 object centre (A): 15.61550 22.47200 3.526000 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 290.3020 centred at (gu) : 90.69553 102.4994 90.57240 assigned negative charge : -285.3022 centred at (gu) : 91.08867 102.8783 90.26566 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 139593 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17729 grid for indexing accessible points = 1.400000 m= 75598 mr = 99897 m= 31434 mr = 63631 m= 7907 mr = 26729 m= 1085 mr = 6173 m= 73 mr = 796 m= 0 mr = 29 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 849 time to turn everything in is 0.8600000 number of dielectric boundary points 58435 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 14668 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) : 1.929330 object centre at (A) : 15.61550 22.47200 3.526000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7165141 -3.6566403E-02 midg,1,midg; midg,igrid,midg 0.3085828 -5.6392293E-02 1,midg,midg; igrid,midg,midg 5.1091976E-02 0.1473621 gauss-seidel spectral radius is 0.9992368 estimated iterations to convergence 286 setup time was (sec) 1.120000 now iterating at: 14:17:03 rms-change max change #iterations 8.566411 337.1026 at 10iterations 4.909965 144.0457 at 20iterations 2.795067 81.03557 at 30iterations 1.591203 36.50516 at 40iterations 0.9084993 21.31898 at 50iterations 0.5158378 10.29616 at 60iterations 0.2943698 6.210802 at 70iterations 0.1675905 3.557892 at 80iterations 9.5190823E-02 1.911474 at 90iterations 5.4124102E-02 1.061327 at 100iterations 3.0736648E-02 0.6089706 at 110iterations 1.7483274E-02 0.3900757 at 120iterations 9.9361446E-03 0.1920166 at 130iterations 5.6428271E-03 0.1158752 at 140iterations 3.2126682E-03 6.3201904E-02 at 150iterations 1.8329889E-03 3.6798596E-02 at 160iterations 1.0387305E-03 2.1575928E-02 at 170iterations 5.9010158E-04 1.3156891E-02 at 180iterations finished qdiffx linear iterations at : 14:17:43 total time elapsed so far: 13.75000 # loops : 180 mean,max change (kT/e) : 5.9010158E-04 1.3156891E-02 energy calculations done at 13.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.89000 DelPhi exited at 14:17:44 13.888u 0.266s 0:47.49 29.7% 0+0k 0+0io 0pf+0w