Tue Oct 11 05:30:23 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 Tue Oct 11 2011 at 05:30:23 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6791042 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): 1.838000 46.77200 ymin,ymax (A): 0.5849999 41.59100 zmin,zma (A): -2.535000 49.88700 x,y,z range (A): 44.93400 41.00600 52.42200 scale (grids/A): 0.6791042 object centre (A): 24.30500 21.08800 23.67600 number of atom coordinates read : 2290 total number of charged atoms : 1965 net assigned charge : 5.564011 assigned positive charge : 319.4260 centred at (gu) : 90.57577 90.26715 89.67337 assigned negative charge : -313.8622 centred at (gu) : 90.71455 90.25787 89.73396 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6495 nv = 96 ne = 84 npr = 42103 no. pairs analyzed = 42103 no. exposed pairs = 2557 no. arc points = 17386 no. surface atoms = 872 nbur = 1418 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 411 mr = 3724 m= 4 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3121 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1744 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7525 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1725826E-08 7.4508915E-09 midg,1,midg; midg,igrid,midg 2.0119533E-08 2.7366696E-08 1,midg,midg; igrid,midg,midg 5.2359255E-08 -1.4469005E-08 gauss-seidel spectral radius is 0.9887058 estimated iterations to convergence 77 setup time was (sec) 0.5100000 now iterating at: 05:30:24 rms-change max change #iterations 0.1713998 26.83572 at 10iterations 1.9956101E-02 3.098076 at 20iterations 2.8483972E-03 0.3609915 at 30iterations 5.6589855E-04 6.7176819E-02 at 40iterations 1.5659843E-04 1.7959595E-02 at 50iterations finished qdiffx linear iterations at : 05:30:26 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.5659843E-04 1.7959595E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 05:30:27 3.351u 0.185s 0:04.02 87.8% 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 Oct 11 2011 at 05:30:27 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.037313 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): 1.838000 46.77200 ymin,ymax (A): 0.5849999 41.59100 zmin,zma (A): -2.535000 49.88700 x,y,z range (A): 44.93400 41.00600 52.42200 scale (grids/A): 2.037313 object centre (A): 24.30500 21.08800 23.67600 number of atom coordinates read : 2290 total number of charged atoms : 1965 net assigned charge : 5.564011 assigned positive charge : 319.4260 centred at (gu) : 91.72749 90.80132 89.02004 assigned negative charge : -313.8622 centred at (gu) : 92.14386 90.77361 89.20214 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69451 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17386 grid for indexing accessible points = 1.400000 m= 27339 mr = 49437 m= 4944 mr = 20646 m= 399 mr = 3186 m= 8 mr = 181 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 28691 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 133 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 15535 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) : 0.6791042 object centre at (A) : 24.30500 21.08800 23.67600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9832931E-02 5.1755801E-02 midg,1,midg; midg,igrid,midg 1.8805346E-03 2.1016575E-02 1,midg,midg; igrid,midg,midg 2.6078306E-02 -4.2941105E-03 gauss-seidel spectral radius is 0.9987432 estimated iterations to convergence 223 setup time was (sec) 0.8200000 now iterating at: 05:30:28 rms-change max change #iterations 4.306940 179.4494 at 10iterations 2.083427 68.50768 at 20iterations 1.010969 35.40470 at 30iterations 0.4872986 16.29005 at 40iterations 0.2368526 7.466770 at 50iterations 0.1149059 3.941271 at 60iterations 5.5819545E-02 1.615312 at 70iterations 2.7252195E-02 0.9377556 at 80iterations 1.3402634E-02 0.4301987 at 90iterations 6.6479831E-03 0.2213049 at 100iterations 3.3699847E-03 0.1030498 at 110iterations 1.7866665E-03 6.3947678E-02 at 120iterations finished qdiffx linear iterations at : 05:30:35 total time elapsed so far: 7.320000 # loops : 120 mean,max change (kT/e) : 1.7866665E-03 6.3947678E-02 energy calculations done at 7.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.500000 DelPhi exited at 05:30:35 7.503u 0.218s 0:08.00 96.3% 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 Oct 11 2011 at 05:30:35 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.055969 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): 1.838000 46.77200 ymin,ymax (A): 0.5849999 41.59100 zmin,zma (A): -2.535000 49.88700 x,y,z range (A): 44.93400 41.00600 52.42200 scale (grids/A): 3.055969 object centre (A): 24.30500 21.08800 23.67600 number of atom coordinates read : 2290 total number of charged atoms : 1965 net assigned charge : 5.564011 assigned positive charge : 319.4260 centred at (gu) : 92.59125 91.20213 88.52998 assigned negative charge : -313.8622 centred at (gu) : 93.21587 91.16053 88.80324 start vw surface at 0.1400000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 160041 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17386 grid for indexing accessible points = 1.400000 m= 86232 mr = 118902 m= 33973 mr = 71698 m= 9226 mr = 27731 m= 1587 mr = 6985 m= 133 mr = 1106 m= 8 mr = 61 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.7900001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.350000 number of dielectric boundary points 64715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 15719 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) : 2.037313 object centre at (A) : 24.30500 21.08800 23.67600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2982539 0.7379843 midg,1,midg; midg,igrid,midg -2.0632235E-02 0.1906290 1,midg,midg; igrid,midg,midg 0.2243283 1.4543229E-03 gauss-seidel spectral radius is 0.9992719 estimated iterations to convergence 292 setup time was (sec) 1.650000 now iterating at: 05:30:37 rms-change max change #iterations 9.797010 310.6880 at 10iterations 5.749744 144.7394 at 20iterations 3.376841 97.02017 at 30iterations 1.973668 43.23351 at 40iterations 1.149402 24.24798 at 50iterations 0.6714028 12.70387 at 60iterations 0.3902547 7.489695 at 70iterations 0.2271407 4.609600 at 80iterations 0.1319868 2.446537 at 90iterations 7.6782674E-02 1.589098 at 100iterations 4.4737864E-02 0.8171768 at 110iterations 2.6238695E-02 0.4995575 at 120iterations 1.5524505E-02 0.2960129 at 130iterations 9.3815131E-03 0.1887817 at 140iterations 5.8287545E-03 0.1260605 at 150iterations 3.7969989E-03 7.3810577E-02 at 160iterations 2.6133310E-03 4.9827576E-02 at 170iterations 1.9058546E-03 3.6235809E-02 at 180iterations finished qdiffx linear iterations at : 05:30:48 total time elapsed so far: 12.80000 # loops : 180 mean,max change (kT/e) : 1.9058546E-03 3.6235809E-02 energy calculations done at 12.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.98000 DelPhi exited at 05:30:49 12.985u 0.235s 0:13.51 97.7% 0+0k 0+0io 0pf+0w