Sat Oct 8 22:48:00 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 22:48:00 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3322 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.5459202 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): -15.78700 40.65800 ymin,ymax (A): 16.42900 76.28700 zmin,zma (A): 22.74600 87.95700 x,y,z range (A): 56.44500 59.85800 65.21100 scale (grids/A): 0.5459202 object centre (A): 12.43550 46.35800 55.35150 number of atom coordinates read : 3322 total number of charged atoms : 3180 net assigned charge : 14.24002 assigned positive charge : 493.3067 centred at (gu) : 89.86032 90.16917 91.09863 assigned negative charge : -479.0683 centred at (gu) : 89.73122 90.23319 91.27625 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6646 nv = 96 ne = 84 npr = 64902 no. pairs analyzed = 64902 no. exposed pairs = 4377 no. arc points = 31710 no. surface atoms = 1461 nbur = 1861 mkacc time = 0.1200000 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= 274 mr = 3328 m= 0 mr = 14 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2300000 number of dielectric boundary points 3578 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3170 ## 407 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8615 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6370159E-09 -5.3411603E-10 midg,1,midg; midg,igrid,midg 1.3020541E-09 4.6078041E-10 1,midg,midg; igrid,midg,midg -3.5231908E-11 1.7490718E-09 gauss-seidel spectral radius is 0.9827397 estimated iterations to convergence 63 setup time was (sec) 0.4400000 now iterating at: 22:48:01 rms-change max change #iterations 7.6879524E-02 14.24478 at 10iterations 5.1415944E-03 0.7975349 at 20iterations 3.7945458E-04 5.9945330E-02 at 30iterations 3.9030121E-05 5.4693222E-03 at 40iterations 6.4306364E-06 6.9141388E-04 at 50iterations finished qdiffx linear iterations at : 22:48:04 total time elapsed so far: 3.580000 # loops : 50 mean,max change (kT/e) : 6.4306364E-06 6.9141388E-04 energy calculations done at 3.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 22:48:04 3.717u 0.214s 0:04.22 92.8% 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 Sat Oct 8 2011 at 22:48:04 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3322 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.637761 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): -15.78700 40.65800 ymin,ymax (A): 16.42900 76.28700 zmin,zma (A): 22.74600 87.95700 x,y,z range (A): 56.44500 59.85800 65.21100 scale (grids/A): 1.637761 object centre (A): 12.43550 46.35800 55.35150 number of atom coordinates read : 3322 total number of charged atoms : 3180 net assigned charge : 14.24002 assigned positive charge : 493.3067 centred at (gu) : 89.58026 90.50694 93.29475 assigned negative charge : -479.0683 centred at (gu) : 89.19351 90.69919 93.82845 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73522 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31710 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 22919 mr = 48793 m= 2405 mr = 15682 m= 71 mr = 1132 m= 0 mr = 6 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 589 time to turn everything in is 0.3600000 number of dielectric boundary points 33304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 357 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 24372 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) : 0.5459202 object centre at (A) : 12.43550 46.35800 55.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6359573E-02 6.2081264E-03 midg,1,midg; midg,igrid,midg 2.6502224E-02 1.4580455E-02 1,midg,midg; igrid,midg,midg -2.9501691E-03 1.1487651E-02 gauss-seidel spectral radius is 0.9982490 estimated iterations to convergence 190 setup time was (sec) 0.6100000 now iterating at: 22:48:05 rms-change max change #iterations 3.534840 152.0554 at 10iterations 1.482410 55.10908 at 20iterations 0.6291769 21.41992 at 30iterations 0.2655837 9.322573 at 40iterations 0.1119340 3.801882 at 50iterations 4.7697283E-02 1.717609 at 60iterations 2.0083582E-02 0.6638265 at 70iterations 8.4893880E-03 0.3047714 at 80iterations 3.5948930E-03 0.1266937 at 90iterations 1.5223891E-03 5.1162720E-02 at 100iterations 6.4782804E-04 2.1440506E-02 at 110iterations 2.7467069E-04 8.8882446E-03 at 120iterations finished qdiffx linear iterations at : 22:48:13 total time elapsed so far: 8.350000 # loops : 120 mean,max change (kT/e) : 2.7467069E-04 8.8882446E-03 energy calculations done at 8.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.480000 DelPhi exited at 22:48:14 8.486u 0.261s 0:09.04 96.6% 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 22:48:14 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3322 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.456641 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): -15.78700 40.65800 ymin,ymax (A): 16.42900 76.28700 zmin,zma (A): 22.74600 87.95700 x,y,z range (A): 56.44500 59.85800 65.21100 scale (grids/A): 2.456641 object centre (A): 12.43550 46.35800 55.35150 number of atom coordinates read : 3322 total number of charged atoms : 3180 net assigned charge : 14.24002 assigned positive charge : 493.3067 centred at (gu) : 89.37013 90.76030 94.94199 assigned negative charge : -479.0683 centred at (gu) : 88.79031 91.04862 95.74268 start vw surface at 0.1000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 170815 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31710 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 78459 mr = 119845 m= 22874 mr = 61516 m= 3691 mr = 17144 m= 280 mr = 2380 m= 7 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 2082 time to turn everything in is 0.9100000 number of dielectric boundary points 75135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 25402 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) : 1.637761 object centre at (A) : 12.43550 46.35800 55.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4358605 7.4597575E-02 midg,1,midg; midg,igrid,midg 0.4493420 0.3404747 1,midg,midg; igrid,midg,midg -2.3828730E-02 0.1670545 gauss-seidel spectral radius is 0.9991730 estimated iterations to convergence 275 setup time was (sec) 1.180000 now iterating at: 22:48:15 rms-change max change #iterations 9.136647 333.6624 at 10iterations 5.213469 149.9937 at 20iterations 2.958267 85.45693 at 30iterations 1.669053 49.16313 at 40iterations 0.9387499 21.30526 at 50iterations 0.5285329 11.45679 at 60iterations 0.2950091 6.773812 at 70iterations 0.1650423 3.848206 at 80iterations 9.2392623E-02 1.852539 at 90iterations 5.1411349E-02 1.191179 at 100iterations 2.8653931E-02 0.5883636 at 110iterations 1.5989758E-02 0.3281622 at 120iterations 8.9128045E-03 0.1848946 at 130iterations 4.9544140E-03 9.0343952E-02 at 140iterations 2.7551912E-03 5.4225922E-02 at 150iterations 1.5330937E-03 3.2445431E-02 at 160iterations 8.5433526E-04 1.6525269E-02 at 170iterations 4.7436464E-04 9.1135502E-03 at 180iterations finished qdiffx linear iterations at : 22:48:27 total time elapsed so far: 13.48000 # loops : 180 mean,max change (kT/e) : 4.7436464E-04 9.1135502E-03 energy calculations done at 13.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.61000 DelPhi exited at 22:48:28 13.614u 0.253s 0:14.19 97.6% 0+0k 0+0io 0pf+0w