Sun Oct 9 13:06:25 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 13:06:25 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 = 2424 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: 0.6793116 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): -15.62000 34.23700 ymin,ymax (A): -13.76000 38.64600 zmin,zma (A): 34.76200 76.95500 x,y,z range (A): 49.85700 52.40600 42.19300 scale (grids/A): 0.6793116 object centre (A): 9.308501 12.44300 55.85850 number of atom coordinates read : 2424 total number of charged atoms : 2282 net assigned charge : 5.500019 assigned positive charge : 371.7719 centred at (gu) : 90.44358 90.89336 89.08289 assigned negative charge : -366.2725 centred at (gu) : 90.46637 91.02410 88.96825 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7265 nv = 96 ne = 84 npr = 49838 no. pairs analyzed = 49838 no. exposed pairs = 2846 no. arc points = 19941 no. surface atoms = 967 nbur = 1457 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 407 mr = 4069 m= 0 mr = 60 time to grow re-entrant surface = 7.9999991E-02 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.1900000 number of dielectric boundary points 3543 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1944 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8583 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3538503E-08 4.8378702E-08 midg,1,midg; midg,igrid,midg 5.2547211E-08 -1.9461408E-08 1,midg,midg; igrid,midg,midg 2.8295291E-08 1.8671305E-08 gauss-seidel spectral radius is 0.9887415 estimated iterations to convergence 77 setup time was (sec) 0.3700000 now iterating at: 13:06:26 rms-change max change #iterations 0.1795705 27.33563 at 10iterations 2.0791467E-02 2.778040 at 20iterations 2.4861319E-03 0.3618744 at 30iterations 3.5592812E-04 4.9650192E-02 at 40iterations 7.3953786E-05 8.4743500E-03 at 50iterations finished qdiffx linear iterations at : 13:06:29 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 7.3953786E-05 8.4743500E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 13:06:29 3.414u 0.436s 0:04.18 91.8% 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 13:06:29 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 = 2424 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: 2.037935 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): -15.62000 34.23700 ymin,ymax (A): -13.76000 38.64600 zmin,zma (A): 34.76200 76.95500 x,y,z range (A): 49.85700 52.40600 42.19300 scale (grids/A): 2.037935 object centre (A): 9.308501 12.44300 55.85850 number of atom coordinates read : 2424 total number of charged atoms : 2282 net assigned charge : 5.500019 assigned positive charge : 371.7719 centred at (gu) : 91.33012 92.67957 87.24814 assigned negative charge : -366.2725 centred at (gu) : 91.39899 93.07188 86.90437 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 77895 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19941 grid for indexing accessible points = 1.400000 m= 28742 mr = 54654 m= 4908 mr = 21375 m= 403 mr = 3113 m= 3 mr = 201 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 83 time to turn everything in is 0.4000000 number of dielectric boundary points 32608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 18060 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) : 0.6793116 object centre at (A) : 9.308501 12.44300 55.85850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0632768E-04 5.1680196E-02 midg,1,midg; midg,igrid,midg 3.6312871E-02 -1.4610936E-02 1,midg,midg; igrid,midg,midg 1.1123240E-02 5.0069254E-02 gauss-seidel spectral radius is 0.9987763 estimated iterations to convergence 226 setup time was (sec) 0.6200000 now iterating at: 13:06:30 rms-change max change #iterations 4.692672 237.1604 at 10iterations 2.283127 104.5289 at 20iterations 1.117600 38.63771 at 30iterations 0.5466098 16.14724 at 40iterations 0.2660879 8.578012 at 50iterations 0.1295527 4.089703 at 60iterations 6.3358963E-02 1.964985 at 70iterations 3.0854544E-02 0.9424624 at 80iterations 1.5176992E-02 0.5019046 at 90iterations 7.4192355E-03 0.2090492 at 100iterations 3.6465111E-03 0.1089869 at 110iterations 1.8033322E-03 5.3468704E-02 at 120iterations finished qdiffx linear iterations at : 13:06:37 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 1.8033322E-03 5.3468704E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 13:06:38 7.872u 0.228s 0:08.46 95.6% 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 Sun Oct 9 2011 at 13:06:38 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 = 2424 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: 3.056902 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): -15.62000 34.23700 ymin,ymax (A): -13.76000 38.64600 zmin,zma (A): 34.76200 76.95500 x,y,z range (A): 49.85700 52.40600 42.19300 scale (grids/A): 3.056902 object centre (A): 9.308501 12.44300 55.85850 number of atom coordinates read : 2424 total number of charged atoms : 2282 net assigned charge : 5.500019 assigned positive charge : 371.7719 centred at (gu) : 91.99527 94.01909 85.87211 assigned negative charge : -366.2725 centred at (gu) : 92.09834 94.60789 85.35655 start vw surface at 0.1000000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 180047 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19941 grid for indexing accessible points = 1.400000 m= 92554 mr = 132243 m= 34430 mr = 76279 m= 8990 mr = 27813 m= 1668 mr = 6766 m= 187 mr = 1193 m= 2 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 246 time to turn everything in is 1.050000 number of dielectric boundary points 73472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 18256 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) : 2.037935 object centre at (A) : 9.308501 12.44300 55.85850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1059964 0.4804359 midg,1,midg; midg,igrid,midg 0.8614907 -4.8653562E-02 1,midg,midg; igrid,midg,midg -8.1768133E-02 0.6525454 gauss-seidel spectral radius is 0.9992856 estimated iterations to convergence 295 setup time was (sec) 1.280000 now iterating at: 13:06:39 rms-change max change #iterations 10.65073 342.5482 at 10iterations 6.266876 132.0607 at 20iterations 3.681443 79.68903 at 30iterations 2.155282 41.19912 at 40iterations 1.264237 24.34149 at 50iterations 0.7378194 14.01134 at 60iterations 0.4298867 7.683466 at 70iterations 0.2508374 4.383854 at 80iterations 0.1462821 2.466898 at 90iterations 8.5155241E-02 1.464692 at 100iterations 4.9703702E-02 0.9926815 at 110iterations 2.8993623E-02 0.5343246 at 120iterations 1.6976999E-02 0.3009501 at 130iterations 9.9378927E-03 0.1913185 at 140iterations 5.8953753E-03 9.9235535E-02 at 150iterations 3.5340653E-03 6.7690849E-02 at 160iterations 2.1654288E-03 4.6983719E-02 at 170iterations 1.3685001E-03 2.8797150E-02 at 180iterations finished qdiffx linear iterations at : 13:06:51 total time elapsed so far: 12.63000 # loops : 180 mean,max change (kT/e) : 1.3685001E-03 2.8797150E-02 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.76000 DelPhi exited at 13:06:51 12.764u 0.259s 0:13.45 96.7% 0+0k 0+0io 0pf+0w