Tue Oct 11 05:26:40 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+sph.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 = amb.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 05:26:40 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2058 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7169470 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): 25.73200 73.03900 ymin,ymax (A): -20.91100 28.74400 zmin,zma (A): 3.866000 46.49800 x,y,z range (A): 47.30700 49.65500 42.63200 scale (grids/A): 0.7169470 object centre (A): 49.38550 3.916500 25.18200 number of atom coordinates read : 2058 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 88.94958 91.51906 90.13287 assigned negative charge : -304.2972 centred at (gu) : 89.06727 91.39582 90.19230 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7269 nv = 96 ne = 84 npr = 41510 no. pairs analyzed = 41510 no. exposed pairs = 2488 no. arc points = 17015 no. surface atoms = 845 nbur = 1213 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 475 mr = 4196 m= 4 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3482 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1601 ## 128 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7904 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0909208E-07 4.2353587E-08 midg,1,midg; midg,igrid,midg 3.1802905E-09 1.9976761E-07 1,midg,midg; igrid,midg,midg 1.7843634E-07 5.8679013E-09 gauss-seidel spectral radius is 0.9898539 estimated iterations to convergence 81 setup time was (sec) 0.3700000 now iterating at: 05:26:40 rms-change max change #iterations 0.2118412 33.47182 at 10iterations 2.6992109E-02 4.355362 at 20iterations 3.7197375E-03 0.5223284 at 30iterations 6.5769523E-04 8.2122803E-02 at 40iterations 1.7563500E-04 2.0433426E-02 at 50iterations finished qdiffx linear iterations at : 05:26:43 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.7563500E-04 2.0433426E-02 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 05:26:44 3.421u 0.174s 0:03.92 91.5% 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 Tue Oct 11 2011 at 05:26:44 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2058 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.150841 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): 25.73200 73.03900 ymin,ymax (A): -20.91100 28.74400 zmin,zma (A): 3.866000 46.49800 x,y,z range (A): 47.30700 49.65500 42.63200 scale (grids/A): 2.150841 object centre (A): 49.38550 3.916500 25.18200 number of atom coordinates read : 2058 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 86.84883 94.55701 90.39828 assigned negative charge : -304.2972 centred at (gu) : 87.20181 94.18749 90.57715 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 76147 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17015 grid for indexing accessible points = 1.400000 m= 32091 mr = 54301 m= 6391 mr = 24634 m= 558 mr = 4291 m= 19 mr = 245 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 31735 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 49 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 15334 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) : 0.7169470 object centre at (A) : 49.38550 3.916500 25.18200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5383547E-02 2.9350020E-02 midg,1,midg; midg,igrid,midg 3.8080055E-02 0.1048534 1,midg,midg; igrid,midg,midg 4.6886437E-02 -3.4819398E-02 gauss-seidel spectral radius is 0.9988559 estimated iterations to convergence 234 setup time was (sec) 0.6300000 now iterating at: 05:26:45 rms-change max change #iterations 4.638375 239.0779 at 10iterations 2.312289 74.94014 at 20iterations 1.156133 35.82051 at 30iterations 0.5796204 16.96965 at 40iterations 0.2901270 8.480377 at 50iterations 0.1450945 4.153885 at 60iterations 7.2659180E-02 2.230043 at 70iterations 3.6431395E-02 1.297799 at 80iterations 1.8320154E-02 0.5240974 at 90iterations 9.2759160E-03 0.2704201 at 100iterations 4.6988018E-03 0.1310425 at 110iterations 2.4533533E-03 7.2837830E-02 at 120iterations finished qdiffx linear iterations at : 05:26:52 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 2.4533533E-03 7.2837830E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 05:26:53 7.971u 0.197s 0:08.71 93.6% 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 Tue Oct 11 2011 at 05:26:53 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2058 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.226261 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): 25.73200 73.03900 ymin,ymax (A): -20.91100 28.74400 zmin,zma (A): 3.866000 46.49800 x,y,z range (A): 47.30700 49.65500 42.63200 scale (grids/A): 3.226261 object centre (A): 49.38550 3.916500 25.18200 number of atom coordinates read : 2058 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 85.27317 96.83558 90.59754 assigned negative charge : -304.2972 centred at (gu) : 85.80278 96.28138 90.86595 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 175457 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17015 grid for indexing accessible points = 1.400000 m= 98062 mr = 130560 m= 41774 mr = 82153 m= 12325 mr = 34656 m= 2281 mr = 9561 m= 244 mr = 1582 m= 14 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 71511 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 15432 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) : 2.150841 object centre at (A) : 49.38550 3.916500 25.18200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1325933 0.2272845 midg,1,midg; midg,igrid,midg 0.2632190 0.8095255 1,midg,midg; igrid,midg,midg 0.3847547 -0.4240455 gauss-seidel spectral radius is 0.9993042 estimated iterations to convergence 299 setup time was (sec) 1.460000 now iterating at: 05:26:54 rms-change max change #iterations 10.30342 333.1503 at 10iterations 6.117152 133.4925 at 20iterations 3.628552 71.41825 at 30iterations 2.149954 42.14055 at 40iterations 1.273247 25.76580 at 50iterations 0.7501615 14.54620 at 60iterations 0.4413743 8.922695 at 70iterations 0.2605932 4.873508 at 80iterations 0.1534096 2.998077 at 90iterations 9.0359800E-02 1.728249 at 100iterations 5.3164616E-02 1.085838 at 110iterations 3.1404242E-02 0.5541680 at 120iterations 1.8618789E-02 0.3164768 at 130iterations 1.1196452E-02 0.1968765 at 140iterations 6.8646148E-03 0.1256428 at 150iterations 4.3524979E-03 7.3989868E-02 at 160iterations 2.9139132E-03 5.2582741E-02 at 170iterations 2.0721643E-03 3.5903931E-02 at 180iterations finished qdiffx linear iterations at : 05:27:06 total time elapsed so far: 12.85000 # loops : 180 mean,max change (kT/e) : 2.0721643E-03 3.5903931E-02 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.99000 DelPhi exited at 05:27:06 12.993u 0.197s 0:13.75 95.8% 0+0k 0+0io 0pf+0w