Tue Oct 11 03:17:30 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 03:17:30 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3271 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5436360 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): 5.999000 62.63100 ymin,ymax (A): -7.260000 58.22500 zmin,zma (A): 58.94800 112.6090 x,y,z range (A): 56.63200 65.48500 53.66100 scale (grids/A): 0.5436360 object centre (A): 34.31500 25.48250 85.77850 number of atom coordinates read : 3271 total number of charged atoms : 3170 net assigned charge : -4.999980 assigned positive charge : 501.9633 centred at (gu) : 91.01737 91.46790 88.53805 assigned negative charge : -506.9648 centred at (gu) : 90.99435 91.51339 88.57681 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 6308 nv = 96 ne = 84 npr = 62958 no. pairs analyzed = 62958 no. exposed pairs = 4959 no. arc points = 34283 no. surface atoms = 1640 nbur = 1631 mkacc time = 0.1900000 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 = 1.596000 m= 255 mr = 2796 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 3759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3367 ## 399 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 8364 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7829493E-11 -3.8575471E-10 midg,1,midg; midg,igrid,midg 1.6630525E-11 -8.6332475E-10 1,midg,midg; igrid,midg,midg -3.4509565E-10 -1.5731054E-10 gauss-seidel spectral radius is 0.9825918 estimated iterations to convergence 62 setup time was (sec) 0.7900000 now iterating at: 03:17:31 rms-change max change #iterations 7.3655576E-02 11.60258 at 10iterations 4.8997435E-03 0.7119751 at 20iterations 4.7536462E-04 9.6878052E-02 at 30iterations 1.0509575E-04 2.3969650E-02 at 40iterations 3.0116013E-05 6.8683624E-03 at 50iterations finished qdiffx linear iterations at : 03:17:34 total time elapsed so far: 4.100000 # loops : 50 mean,max change (kT/e) : 3.0116013E-05 6.8683624E-03 energy calculations done at 4.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.340000 DelPhi exited at 03:17:35 4.339u 0.175s 0:04.91 91.6% 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 03:17:35 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3271 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.630908 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): 5.999000 62.63100 ymin,ymax (A): -7.260000 58.22500 zmin,zma (A): 58.94800 112.6090 x,y,z range (A): 56.63200 65.48500 53.66100 scale (grids/A): 1.630908 object centre (A): 34.31500 25.48250 85.77850 number of atom coordinates read : 3271 total number of charged atoms : 3170 net assigned charge : -4.999980 assigned positive charge : 501.9633 centred at (gu) : 93.05099 94.40255 85.61320 assigned negative charge : -506.9648 centred at (gu) : 92.98252 94.53960 85.72974 start vw surface at 0.2300000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 68728 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34283 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 20152 mr = 42510 m= 2084 mr = 12659 m= 60 mr = 884 m= 0 mr = 5 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 34966 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 332 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 24285 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) : 0.5436360 object centre at (A) : 34.31500 25.48250 85.77850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0731722E-02 -1.7412597E-03 midg,1,midg; midg,igrid,midg 3.2869915E-03 -5.1316965E-02 1,midg,midg; igrid,midg,midg -1.5362531E-02 -1.2317729E-02 gauss-seidel spectral radius is 0.9982346 estimated iterations to convergence 189 setup time was (sec) 1.060000 now iterating at: 03:17:36 rms-change max change #iterations 3.568457 155.3577 at 10iterations 1.504457 67.71980 at 20iterations 0.6323143 22.87959 at 30iterations 0.2662349 9.911662 at 40iterations 0.1120234 4.043254 at 50iterations 4.7093973E-02 1.653444 at 60iterations 1.9866239E-02 0.7377272 at 70iterations 8.4163863E-03 0.3023500 at 80iterations 3.5816035E-03 0.1392765 at 90iterations 1.5239675E-03 5.3607941E-02 at 100iterations 6.6332688E-04 2.7165413E-02 at 110iterations 2.9960813E-04 1.1514664E-02 at 120iterations finished qdiffx linear iterations at : 03:17:45 total time elapsed so far: 9.370000 # loops : 120 mean,max change (kT/e) : 2.9960813E-04 1.1514664E-02 energy calculations done at 9.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.590000 DelPhi exited at 03:17:45 9.597u 0.246s 0:10.32 95.2% 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 Tue Oct 11 2011 at 03:17:46 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3271 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.446362 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): 5.999000 62.63100 ymin,ymax (A): -7.260000 58.22500 zmin,zma (A): 58.94800 112.6090 x,y,z range (A): 56.63200 65.48500 53.66100 scale (grids/A): 2.446362 object centre (A): 34.31500 25.48250 85.77850 number of atom coordinates read : 3271 total number of charged atoms : 3170 net assigned charge : -4.999980 assigned positive charge : 501.9633 centred at (gu) : 94.57621 96.60359 83.41948 assigned negative charge : -506.9648 centred at (gu) : 94.47372 96.80920 83.59438 start vw surface at 0.2200000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 159489 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34283 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 68446 mr = 105565 m= 19858 mr = 50662 m= 3174 mr = 14043 m= 241 mr = 1872 m= 3 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.630000 number of dielectric boundary points 78968 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 25332 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) : 1.630908 object centre at (A) : 34.31500 25.48250 85.77850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1747300 -9.9387718E-03 midg,1,midg; midg,igrid,midg 0.3044835 -1.015924 1,midg,midg; igrid,midg,midg -0.2445610 -0.1844078 gauss-seidel spectral radius is 0.9991868 estimated iterations to convergence 277 setup time was (sec) 2.020000 now iterating at: 03:17:48 rms-change max change #iterations 9.655008 346.1700 at 10iterations 5.670308 156.5171 at 20iterations 3.285296 92.89326 at 30iterations 1.883947 46.07814 at 40iterations 1.076718 26.84469 at 50iterations 0.6133272 14.22311 at 60iterations 0.3483249 7.627939 at 70iterations 0.1966502 4.177158 at 80iterations 0.1107263 2.366772 at 90iterations 6.2438354E-02 1.312156 at 100iterations 3.5164531E-02 0.7529602 at 110iterations 1.9770125E-02 0.4254424 at 120iterations 1.1117584E-02 0.2224655 at 130iterations 6.2518693E-03 0.1335040 at 140iterations 3.5245828E-03 7.7194214E-02 at 150iterations 1.9911046E-03 4.3769836E-02 at 160iterations 1.1336671E-03 2.4028778E-02 at 170iterations 6.5452710E-04 1.4693260E-02 at 180iterations finished qdiffx linear iterations at : 03:18:01 total time elapsed so far: 15.22000 # loops : 180 mean,max change (kT/e) : 6.5452710E-04 1.4693260E-02 energy calculations done at 15.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.46000 DelPhi exited at 03:18:02 15.466u 0.245s 0:16.07 97.6% 0+0k 0+0io 0pf+0w