Mon Oct 10 13:59:03 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 Mon Oct 10 2011 at 13:59:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4432 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: 0.5049145 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): -3.394000 67.11300 ymin,ymax (A): -12.35100 38.34800 zmin,zma (A): -20.07200 45.26700 x,y,z range (A): 70.50700 50.69901 65.33900 scale (grids/A): 0.5049145 object centre (A): 31.85950 12.99850 12.59750 number of atom coordinates read : 4432 total number of charged atoms : 4277 net assigned charge : -4.999953 assigned positive charge : 670.2787 centred at (gu) : 88.04302 89.86983 90.81535 assigned negative charge : -675.2812 centred at (gu) : 88.11299 89.99038 90.84081 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6964 nv = 96 ne = 84 npr = 93316 no. pairs analyzed = 93316 no. exposed pairs = 5030 no. arc points = 33876 no. surface atoms = 1722 nbur = 2710 mkacc time = 0.1600000 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 = 1.680000 m= 243 mr = 3856 m= 0 mr = 10 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2900000 number of dielectric boundary points 3341 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3418 ## 514 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 9503 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.4918067E-12 -1.3164314E-10 midg,1,midg; midg,igrid,midg 1.7522189E-10 -2.8108099E-10 1,midg,midg; igrid,midg,midg 1.3028921E-10 -1.1454429E-10 gauss-seidel spectral radius is 0.9799065 estimated iterations to convergence 58 setup time was (sec) 0.4800000 now iterating at: 13:59:04 rms-change max change #iterations 6.1891288E-02 10.29418 at 10iterations 3.4571739E-03 0.5506439 at 20iterations 3.7260650E-04 5.4854393E-02 at 30iterations 8.8407236E-05 1.2736797E-02 at 40iterations 2.3732686E-05 3.5986900E-03 at 50iterations finished qdiffx linear iterations at : 13:59:07 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 2.3732686E-05 3.5986900E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 13:59:07 3.546u 0.186s 0:04.17 89.2% 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 Mon Oct 10 2011 at 13:59:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4432 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: 1.514743 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): -3.394000 67.11300 ymin,ymax (A): -12.35100 38.34800 zmin,zma (A): -20.07200 45.26700 x,y,z range (A): 70.50700 50.69901 65.33900 scale (grids/A): 1.514743 object centre (A): 31.85950 12.99850 12.59750 number of atom coordinates read : 4432 total number of charged atoms : 4277 net assigned charge : -4.999953 assigned positive charge : 670.2787 centred at (gu) : 84.12799 89.60846 92.44481 assigned negative charge : -675.2812 centred at (gu) : 84.33855 89.97073 92.52187 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 79981 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33876 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23646 mr = 57340 m= 2100 mr = 16381 m= 30 mr = 976 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 897 time to turn everything in is 0.4200000 number of dielectric boundary points 31060 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 495 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 32026 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) : 0.5049145 object centre at (A) : 31.85950 12.99850 12.59750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.3321176E-03 -1.0099888E-02 midg,1,midg; midg,igrid,midg 3.2314244E-03 -9.8688146E-03 1,midg,midg; igrid,midg,midg 1.3661576E-02 -3.7486262E-03 gauss-seidel spectral radius is 0.9980064 estimated iterations to convergence 178 setup time was (sec) 0.6300000 now iterating at: 13:59:08 rms-change max change #iterations 3.542835 159.7847 at 10iterations 1.415851 49.71366 at 20iterations 0.5668668 18.17902 at 30iterations 0.2278761 7.468380 at 40iterations 9.1229886E-02 3.219280 at 50iterations 3.6721576E-02 1.188185 at 60iterations 1.4805698E-02 0.4811225 at 70iterations 5.9979428E-03 0.1948032 at 80iterations 2.4689490E-03 7.5416565E-02 at 90iterations 1.0521660E-03 3.6075592E-02 at 100iterations 4.7484785E-04 1.6497612E-02 at 110iterations 2.3649678E-04 8.4152222E-03 at 120iterations finished qdiffx linear iterations at : 13:59:15 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 2.3649678E-04 8.4152222E-03 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 13:59:16 7.942u 0.192s 0:08.62 94.3% 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 13:59:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4432 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: 2.272115 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): -3.394000 67.11300 ymin,ymax (A): -12.35100 38.34800 zmin,zma (A): -20.07200 45.26700 x,y,z range (A): 70.50700 50.69901 65.33900 scale (grids/A): 2.272115 object centre (A): 31.85950 12.99850 12.59750 number of atom coordinates read : 4432 total number of charged atoms : 4277 net assigned charge : -4.999953 assigned positive charge : 670.2787 centred at (gu) : 81.19161 89.41254 93.66671 assigned negative charge : -675.2812 centred at (gu) : 81.50774 89.95605 93.78265 start vw surface at 0.1300000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 186833 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33876 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 85254 mr = 140348 m= 21701 mr = 68441 m= 2990 mr = 16096 m= 116 mr = 1921 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 2875 time to turn everything in is 0.9700000 number of dielectric boundary points 70078 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 90 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 34125 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) : 1.514743 object centre at (A) : 31.85950 12.99850 12.59750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2521889 -0.2319460 midg,1,midg; midg,igrid,midg 3.8422190E-02 -0.1601789 1,midg,midg; igrid,midg,midg 0.3396938 -0.3778726 gauss-seidel spectral radius is 0.9991056 estimated iterations to convergence 264 setup time was (sec) 1.210000 now iterating at: 13:59:17 rms-change max change #iterations 9.541915 320.1526 at 10iterations 5.320591 112.8215 at 20iterations 2.948194 60.92392 at 30iterations 1.627431 33.49487 at 40iterations 0.8911306 17.57439 at 50iterations 0.4888460 10.30692 at 60iterations 0.2675320 5.794942 at 70iterations 0.1461379 3.238319 at 80iterations 7.9649001E-02 1.604516 at 90iterations 4.3393973E-02 0.8130178 at 100iterations 2.3696901E-02 0.4651651 at 110iterations 1.2924979E-02 0.2315807 at 120iterations 7.0417398E-03 0.1378756 at 130iterations 3.8277230E-03 7.4028492E-02 at 140iterations 2.0920972E-03 4.2397499E-02 at 150iterations 1.1437569E-03 2.1556854E-02 at 160iterations 6.2769797E-04 1.2384415E-02 at 170iterations 3.4763847E-04 6.3209534E-03 at 180iterations finished qdiffx linear iterations at : 13:59:30 total time elapsed so far: 13.61000 # loops : 180 mean,max change (kT/e) : 3.4763847E-04 6.3209534E-03 energy calculations done at 13.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.74000 DelPhi exited at 13:59:31 13.746u 0.210s 0:14.80 94.2% 0+0k 0+0io 0pf+0w