Mon Oct 10 14:07:43 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 Mon Oct 10 2011 at 14:07:43 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3867 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: 0.5423853 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): -4.807000 55.89800 ymin,ymax (A): -27.11400 38.52200 zmin,zma (A): -10.66500 41.99200 x,y,z range (A): 60.70500 65.63600 52.65700 scale (grids/A): 0.5423853 object centre (A): 25.54550 5.704001 15.66350 number of atom coordinates read : 3867 total number of charged atoms : 3723 net assigned charge : -3.499993 assigned positive charge : 599.1671 centred at (gu) : 91.26572 91.02649 91.08652 assigned negative charge : -602.6697 centred at (gu) : 91.22740 91.11337 90.97213 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7380 nv = 96 ne = 84 npr = 77514 no. pairs analyzed = 77514 no. exposed pairs = 4954 no. arc points = 33980 no. surface atoms = 1670 nbur = 2197 mkacc time = 0.1400000 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= 301 mr = 3834 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2800000 number of dielectric boundary points 3826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3426 ## 426 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 9715 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.4182733E-10 9.1152547E-10 midg,1,midg; midg,igrid,midg 3.6782064E-10 -1.1444947E-09 1,midg,midg; igrid,midg,midg -3.6322478E-10 1.4743905E-10 gauss-seidel spectral radius is 0.9825453 estimated iterations to convergence 62 setup time was (sec) 0.4800000 now iterating at: 14:07:44 rms-change max change #iterations 8.3542287E-02 12.75185 at 10iterations 6.0092784E-03 0.8882885 at 20iterations 8.1020565E-04 0.1487370 at 30iterations 1.9988726E-04 3.9073944E-02 at 40iterations 5.6247838E-05 1.0707855E-02 at 50iterations finished qdiffx linear iterations at : 14:07:47 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 5.6247838E-05 1.0707855E-02 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 14:07:47 3.471u 0.208s 0:04.20 87.3% 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 Mon Oct 10 2011 at 14:07:47 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3867 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: 1.627156 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): -4.807000 55.89800 ymin,ymax (A): -27.11400 38.52200 zmin,zma (A): -10.66500 41.99200 x,y,z range (A): 60.70500 65.63600 52.65700 scale (grids/A): 1.627156 object centre (A): 25.54550 5.704001 15.66350 number of atom coordinates read : 3867 total number of charged atoms : 3723 net assigned charge : -3.499993 assigned positive charge : 599.1671 centred at (gu) : 93.79621 93.07830 93.25801 assigned negative charge : -602.6697 centred at (gu) : 93.68203 93.33992 92.91630 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 82473 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33980 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 25313 mr = 56671 m= 2752 mr = 16975 m= 80 mr = 1295 m= 0 mr = 12 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 821 time to turn everything in is 0.4100000 number of dielectric boundary points 35665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 343 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 28506 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) : 0.5423853 object centre at (A) : 25.54550 5.704001 15.66350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5688021E-02 -4.6648863E-03 midg,1,midg; midg,igrid,midg 2.3221435E-02 -9.8493230E-03 1,midg,midg; igrid,midg,midg 3.8053419E-03 -8.0326218E-03 gauss-seidel spectral radius is 0.9982683 estimated iterations to convergence 191 setup time was (sec) 0.6300000 now iterating at: 14:07:48 rms-change max change #iterations 3.920195 153.9827 at 10iterations 1.660291 54.66703 at 20iterations 0.7096815 24.03491 at 30iterations 0.3025744 9.435808 at 40iterations 0.1286788 4.148819 at 50iterations 5.4832086E-02 1.946622 at 60iterations 2.3403045E-02 0.7215010 at 70iterations 1.0036671E-02 0.3496656 at 80iterations 4.3286164E-03 0.1377754 at 90iterations 1.8931630E-03 6.0169220E-02 at 100iterations 8.5122540E-04 3.1169415E-02 at 110iterations 4.0461015E-04 1.4469147E-02 at 120iterations finished qdiffx linear iterations at : 14:07:55 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 4.0461015E-04 1.4469147E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 14:07:56 7.771u 0.257s 0:08.48 94.5% 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 Mon Oct 10 2011 at 14:07:56 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3867 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: 2.440734 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): -4.807000 55.89800 ymin,ymax (A): -27.11400 38.52200 zmin,zma (A): -10.66500 41.99200 x,y,z range (A): 60.70500 65.63600 52.65700 scale (grids/A): 2.440734 object centre (A): 25.54550 5.704001 15.66350 number of atom coordinates read : 3867 total number of charged atoms : 3723 net assigned charge : -3.499993 assigned positive charge : 599.1671 centred at (gu) : 95.69395 94.61715 94.88660 assigned negative charge : -602.6697 centred at (gu) : 95.52289 95.00955 94.37429 start vw surface at 0.1200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 191964 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33980 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 88024 mr = 139275 m= 24854 mr = 68591 m= 4227 mr = 18187 m= 299 mr = 2717 m= 10 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 2678 time to turn everything in is 1.060000 number of dielectric boundary points 80474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 29750 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) : 1.627156 object centre at (A) : 25.54550 5.704001 15.66350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2216480 -0.1179226 midg,1,midg; midg,igrid,midg 0.6411019 -0.2182599 1,midg,midg; igrid,midg,midg 0.1127634 -0.1843703 gauss-seidel spectral radius is 0.9991864 estimated iterations to convergence 277 setup time was (sec) 1.330000 now iterating at: 14:07:58 rms-change max change #iterations 10.32228 343.3188 at 10iterations 5.933535 134.2516 at 20iterations 3.403811 98.51696 at 30iterations 1.940434 45.90756 at 40iterations 1.099741 21.22976 at 50iterations 0.6238015 12.91254 at 60iterations 0.3514504 6.585146 at 70iterations 0.1984172 3.480412 at 80iterations 0.1115786 2.053238 at 90iterations 6.2761858E-02 1.225874 at 100iterations 3.5296105E-02 0.6590347 at 110iterations 1.9839190E-02 0.3567581 at 120iterations 1.1144748E-02 0.2142553 at 130iterations 6.2506860E-03 0.1197205 at 140iterations 3.5199607E-03 6.6975117E-02 at 150iterations 1.9837432E-03 3.5869598E-02 at 160iterations 1.1236487E-03 2.0431519E-02 at 170iterations 6.4202561E-04 1.3161182E-02 at 180iterations finished qdiffx linear iterations at : 14:08:09 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 6.4202561E-04 1.3161182E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 14:08:10 12.736u 0.243s 0:13.82 93.8% 0+0k 0+0io 0pf+0w