Sun Oct 9 05:26:52 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 05:26:52 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2209 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: 0.6565238 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): 31.65000 77.93501 ymin,ymax (A): -2.352000 51.87300 zmin,zma (A): -11.63800 30.16000 x,y,z range (A): 46.28500 54.22500 41.79800 scale (grids/A): 0.6565238 object centre (A): 54.79250 24.76050 9.261000 number of atom coordinates read : 2209 total number of charged atoms : 2053 net assigned charge : 0.5000157 assigned positive charge : 298.3751 centred at (gu) : 90.77886 90.26645 90.19529 assigned negative charge : -297.8754 centred at (gu) : 90.82492 90.34090 90.27925 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6438 nv = 96 ne = 84 npr = 47340 no. pairs analyzed = 47340 no. exposed pairs = 2785 no. arc points = 19817 no. surface atoms = 952 nbur = 1257 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 409 mr = 3391 m= 3 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1659 ## 87 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7378 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2309582E-08 -1.0929956E-08 midg,1,midg; midg,igrid,midg 1.0898774E-08 -9.6770041E-09 1,midg,midg; igrid,midg,midg 6.4855183E-09 -6.0941101E-09 gauss-seidel spectral radius is 0.9879485 estimated iterations to convergence 74 setup time was (sec) 0.5900000 now iterating at: 05:26:53 rms-change max change #iterations 0.1422355 23.44488 at 10iterations 1.4575828E-02 2.248178 at 20iterations 1.6828073E-03 0.2439957 at 30iterations 2.7411940E-04 4.3278217E-02 at 40iterations 7.3163967E-05 1.1326432E-02 at 50iterations finished qdiffx linear iterations at : 05:26:56 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 7.3163967E-05 1.1326432E-02 energy calculations done at 3.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.040000 DelPhi exited at 05:26:57 4.045u 0.256s 0:04.61 93.0% 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 05:26:57 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2209 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: 1.969571 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): 31.65000 77.93501 ymin,ymax (A): -2.352000 51.87300 zmin,zma (A): -11.63800 30.16000 x,y,z range (A): 46.28500 54.22500 41.79800 scale (grids/A): 1.969571 object centre (A): 54.79250 24.76050 9.261000 number of atom coordinates read : 2209 total number of charged atoms : 2053 net assigned charge : 0.5000157 assigned positive charge : 298.3751 centred at (gu) : 92.33667 90.79952 90.58582 assigned negative charge : -297.8754 centred at (gu) : 92.47510 91.02305 90.83791 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 69072 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19817 grid for indexing accessible points = 1.400000 m= 25337 mr = 46617 m= 4556 mr = 18332 m= 268 mr = 2854 m= 3 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 231 time to turn everything in is 0.6300000 number of dielectric boundary points 31357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 61 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 16259 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) : 0.6565238 object centre at (A) : 54.79250 24.76050 9.261000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6639043E-02 3.8329782E-03 midg,1,midg; midg,igrid,midg -4.3997834E-03 -3.4367319E-02 1,midg,midg; igrid,midg,midg 6.6082510E-03 -1.6307810E-03 gauss-seidel spectral radius is 0.9986933 estimated iterations to convergence 219 setup time was (sec) 0.9400000 now iterating at: 05:26:58 rms-change max change #iterations 3.955514 163.1220 at 10iterations 1.884013 70.33754 at 20iterations 0.8944451 31.73515 at 30iterations 0.4255208 14.81608 at 40iterations 0.2029185 6.427879 at 50iterations 9.6791565E-02 3.337009 at 60iterations 4.5970887E-02 1.614326 at 70iterations 2.1942981E-02 0.6909122 at 80iterations 1.0494645E-02 0.3423681 at 90iterations 5.0211209E-03 0.1774335 at 100iterations 2.4262802E-03 7.6446533E-02 at 110iterations 1.1847361E-03 4.1991949E-02 at 120iterations finished qdiffx linear iterations at : 05:27:06 total time elapsed so far: 9.200000 # loops : 120 mean,max change (kT/e) : 1.1847361E-03 4.1991949E-02 energy calculations done at 9.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.370000 DelPhi exited at 05:27:07 9.371u 0.301s 0:09.99 96.7% 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 05:27:07 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2209 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: 2.954357 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): 31.65000 77.93501 ymin,ymax (A): -2.352000 51.87300 zmin,zma (A): -11.63800 30.16000 x,y,z range (A): 46.28500 54.22500 41.79800 scale (grids/A): 2.954357 object centre (A): 54.79250 24.76050 9.261000 number of atom coordinates read : 2209 total number of charged atoms : 2053 net assigned charge : 0.5000157 assigned positive charge : 298.3751 centred at (gu) : 93.50503 91.19925 90.87866 assigned negative charge : -297.8754 centred at (gu) : 93.71272 91.53458 91.25704 start vw surface at 0.1400000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 159643 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19817 grid for indexing accessible points = 1.400000 m= 79728 mr = 113379 m= 31054 mr = 64300 m= 8253 mr = 24535 m= 1226 mr = 6273 m= 52 mr = 772 m= 0 mr = 10 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 824 time to turn everything in is 1.640000 number of dielectric boundary points 70687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 16423 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) : 1.969571 object centre at (A) : 54.79250 24.76050 9.261000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1619557 5.5785537E-02 midg,1,midg; midg,igrid,midg 2.6324190E-02 -0.2495706 1,midg,midg; igrid,midg,midg 5.2141268E-02 -9.5963730E-03 gauss-seidel spectral radius is 0.9992695 estimated iterations to convergence 292 setup time was (sec) 1.950000 now iterating at: 05:27:09 rms-change max change #iterations 8.959467 487.6879 at 10iterations 5.171196 115.6913 at 20iterations 2.980472 59.92310 at 30iterations 1.719508 33.67694 at 40iterations 0.9905242 19.03541 at 50iterations 0.5710840 10.86598 at 60iterations 0.3286392 5.736914 at 70iterations 0.1892874 3.422552 at 80iterations 0.1091832 1.912369 at 90iterations 6.3011102E-02 1.172683 at 100iterations 3.6178958E-02 0.6639788 at 110iterations 2.0874593E-02 0.3799102 at 120iterations 1.2037623E-02 0.2191358 at 130iterations 6.9652237E-03 0.1248169 at 140iterations 4.0376312E-03 7.3112488E-02 at 150iterations 2.3630247E-03 4.3407440E-02 at 160iterations 1.3887585E-03 2.4566650E-02 at 170iterations 8.3848776E-04 1.5605450E-02 at 180iterations finished qdiffx linear iterations at : 05:27:23 total time elapsed so far: 15.50000 # loops : 180 mean,max change (kT/e) : 8.3848776E-04 1.5605450E-02 energy calculations done at 15.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.68000 DelPhi exited at 05:27:23 15.681u 0.310s 0:16.26 98.3% 0+0k 0+0io 0pf+0w