Sun Oct 9 01:48:42 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 Sun Oct 9 2011 at 01:48:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2324 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: 0.6659682 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): -27.15800 26.29800 ymin,ymax (A): 8.387000 50.73200 zmin,zma (A): -12.48300 39.82200 x,y,z range (A): 53.45600 42.34500 52.30500 scale (grids/A): 0.6659682 object centre (A): -0.4299994 29.55950 13.66950 number of atom coordinates read : 2324 total number of charged atoms : 2189 net assigned charge : 11.00002 assigned positive charge : 336.9164 centred at (gu) : 90.35119 91.25670 91.73564 assigned negative charge : -325.9171 centred at (gu) : 90.37924 91.20875 91.69887 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7169 nv = 96 ne = 84 npr = 46485 no. pairs analyzed = 46485 no. exposed pairs = 3069 no. arc points = 21968 no. surface atoms = 1032 nbur = 1292 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 460 mr = 3831 m= 6 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.2800000 number of dielectric boundary points 3738 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2021 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8192 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8090839E-08 5.6136770E-08 midg,1,midg; midg,igrid,midg 1.8166620E-08 5.3680548E-08 1,midg,midg; igrid,midg,midg 3.5234958E-08 2.8932316E-08 gauss-seidel spectral radius is 0.9882966 estimated iterations to convergence 75 setup time was (sec) 0.5400000 now iterating at: 01:48:43 rms-change max change #iterations 0.1590424 24.18352 at 10iterations 1.6950177E-02 2.543168 at 20iterations 1.9492010E-03 0.2661103 at 30iterations 3.0106650E-04 4.7381401E-02 at 40iterations 7.8904668E-05 1.4780045E-02 at 50iterations finished qdiffx linear iterations at : 01:48:47 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 7.8904668E-05 1.4780045E-02 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 01:48:47 4.119u 0.227s 0:04.72 91.7% 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 Sun Oct 9 2011 at 01:48:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2324 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: 1.997905 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): -27.15800 26.29800 ymin,ymax (A): 8.387000 50.73200 zmin,zma (A): -12.48300 39.82200 x,y,z range (A): 53.45600 42.34500 52.30500 scale (grids/A): 1.997905 object centre (A): -0.4299994 29.55950 13.66950 number of atom coordinates read : 2324 total number of charged atoms : 2189 net assigned charge : 11.00002 assigned positive charge : 336.9164 centred at (gu) : 91.05299 93.76968 95.20686 assigned negative charge : -325.9171 centred at (gu) : 91.13786 93.62638 95.09663 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75666 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21968 grid for indexing accessible points = 1.400000 m= 28163 mr = 51010 m= 5284 mr = 20587 m= 438 mr = 3449 m= 4 mr = 184 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 562 time to turn everything in is 0.6000000 number of dielectric boundary points 34325 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 17331 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) : 0.6659682 object centre at (A) : -0.4299994 29.55950 13.66950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2451300E-02 4.0112022E-02 midg,1,midg; midg,igrid,midg 4.6977983E-03 3.2145526E-02 1,midg,midg; igrid,midg,midg 6.1400570E-02 6.0528964E-02 gauss-seidel spectral radius is 0.9987361 estimated iterations to convergence 223 setup time was (sec) 0.9400000 now iterating at: 01:48:48 rms-change max change #iterations 4.219779 206.2907 at 10iterations 2.030503 75.24208 at 20iterations 0.9736072 32.38436 at 30iterations 0.4690787 14.69144 at 40iterations 0.2249869 7.511557 at 50iterations 0.1085744 3.305321 at 60iterations 5.2406549E-02 1.507113 at 70iterations 2.5241544E-02 0.8708892 at 80iterations 1.2212486E-02 0.3871610 at 90iterations 5.8880756E-03 0.1865807 at 100iterations 2.8701797E-03 9.0414047E-02 at 110iterations 1.4188185E-03 4.5272827E-02 at 120iterations finished qdiffx linear iterations at : 01:48:57 total time elapsed so far: 9.450000 # loops : 120 mean,max change (kT/e) : 1.4188185E-03 4.5272827E-02 energy calculations done at 9.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.620000 DelPhi exited at 01:48:58 9.625u 0.275s 0:10.44 94.7% 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 Sun Oct 9 2011 at 01:48:58 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 = 2324 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: 2.996857 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): -27.15800 26.29800 ymin,ymax (A): 8.387000 50.73200 zmin,zma (A): -12.48300 39.82200 x,y,z range (A): 53.45600 42.34500 52.30500 scale (grids/A): 2.996857 object centre (A): -0.4299994 29.55950 13.66950 number of atom coordinates read : 2324 total number of charged atoms : 2189 net assigned charge : 11.00002 assigned positive charge : 336.9164 centred at (gu) : 91.57930 95.65437 97.81019 assigned negative charge : -325.9171 centred at (gu) : 91.70679 95.43961 97.64488 start vw surface at 0.1800000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 174987 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21968 grid for indexing accessible points = 1.400000 m= 88379 mr = 124167 m= 34755 mr = 71604 m= 9826 mr = 27940 m= 1908 mr = 7526 m= 122 mr = 1360 m= 3 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 1871 time to turn everything in is 1.590000 number of dielectric boundary points 77346 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 17511 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) : 1.997905 object centre at (A) : -0.4299994 29.55950 13.66950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5021637 0.3947740 midg,1,midg; midg,igrid,midg 1.8535478E-02 0.2865077 1,midg,midg; igrid,midg,midg 0.5775612 0.6046982 gauss-seidel spectral radius is 0.9992924 estimated iterations to convergence 297 setup time was (sec) 1.930000 now iterating at: 01:49:00 rms-change max change #iterations 9.880584 407.3213 at 10iterations 5.858016 141.2739 at 20iterations 3.465435 71.81445 at 30iterations 2.045073 43.16689 at 40iterations 1.202831 24.97861 at 50iterations 0.7060494 13.87954 at 60iterations 0.4140666 8.295473 at 70iterations 0.2425537 4.401314 at 80iterations 0.1418363 2.734795 at 90iterations 8.3008513E-02 1.589984 at 100iterations 4.8418365E-02 0.9242363 at 110iterations 2.8315289E-02 0.5494657 at 120iterations 1.6550628E-02 0.2993164 at 130iterations 9.6835960E-03 0.1653137 at 140iterations 5.6743822E-03 0.1107903 at 150iterations 3.3514004E-03 6.4483166E-02 at 160iterations 1.9982471E-03 3.8883209E-02 at 170iterations 1.2207899E-03 2.3849487E-02 at 180iterations finished qdiffx linear iterations at : 01:49:13 total time elapsed so far: 15.33000 # loops : 180 mean,max change (kT/e) : 1.2207899E-03 2.3849487E-02 energy calculations done at 15.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.52000 DelPhi exited at 01:49:14 15.520u 0.269s 0:16.05 98.3% 0+0k 0+0io 0pf+0w