Tue Oct 11 07:01:17 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 Tue Oct 11 2011 at 07:01:17 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2962 !!! WARNING: UMP 317 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5781755 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): -60.28500 1.288000 ymin,ymax (A): -12.56500 41.05700 zmin,zma (A): 6.327000 54.74800 x,y,z range (A): 61.57300 53.62200 48.42100 scale (grids/A): 0.5781755 object centre (A): -29.49850 14.24600 30.53750 number of atom coordinates read : 2962 total number of charged atoms : 2819 net assigned charge : -3.599983 assigned positive charge : 431.7266 centred at (gu) : 88.97767 88.70689 90.08798 assigned negative charge : -435.3271 centred at (gu) : 89.12447 88.91663 90.09586 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6609 nv = 96 ne = 84 npr = 61044 no. pairs analyzed = 61044 no. exposed pairs = 3752 no. arc points = 26117 no. surface atoms = 1271 nbur = 1691 mkacc time = 0.1300000 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 = 1.484000 m= 296 mr = 3529 m= 3 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.3200000 number of dielectric boundary points 3359 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2637 ## 267 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8320 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.5201006E-10 -1.0042311E-09 midg,1,midg; midg,igrid,midg 4.5470556E-09 -3.8195456E-09 1,midg,midg; igrid,midg,midg 2.6935310E-09 -3.0268152E-09 gauss-seidel spectral radius is 0.9845621 estimated iterations to convergence 66 setup time was (sec) 0.5400000 now iterating at: 07:01:18 rms-change max change #iterations 9.4342709E-02 13.71773 at 10iterations 7.2859796E-03 1.071358 at 20iterations 5.6680909E-04 8.2998276E-02 at 30iterations 4.4244476E-05 6.0539246E-03 at 40iterations 3.5981709E-06 5.9890747E-04 at 50iterations finished qdiffx linear iterations at : 07:01:21 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 3.5981709E-06 5.9890747E-04 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 07:01:21 3.297u 0.191s 0:03.97 87.6% 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 07:01:22 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2962 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 1.734527 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): -60.28500 1.288000 ymin,ymax (A): -12.56500 41.05700 zmin,zma (A): 6.327000 54.74800 x,y,z range (A): 61.57300 53.62200 48.42100 scale (grids/A): 1.734527 object centre (A): -29.49850 14.24600 30.53750 number of atom coordinates read : 2962 total number of charged atoms : 2819 net assigned charge : -3.599983 assigned positive charge : 431.7266 centred at (gu) : 86.93247 86.12031 90.26332 assigned negative charge : -435.3271 centred at (gu) : 87.37314 86.74930 90.28707 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71441 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26117 grid for indexing accessible points = 1.400000 m= 25596 mr = 48896 m= 3471 mr = 18600 m= 128 mr = 2044 m= 0 mr = 9 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 31087 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 21927 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) : 0.5781755 object centre at (A) : -29.49850 14.24600 30.53750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1473478E-02 1.3292500E-02 midg,1,midg; midg,igrid,midg 1.3161237E-02 -3.5986453E-02 1,midg,midg; igrid,midg,midg -2.2626724E-03 -4.3144677E-02 gauss-seidel spectral radius is 0.9984009 estimated iterations to convergence 198 setup time was (sec) 0.8000000 now iterating at: 07:01:23 rms-change max change #iterations 3.709492 154.0406 at 10iterations 1.629343 63.05555 at 20iterations 0.7157267 25.81979 at 30iterations 0.3163658 9.773541 at 40iterations 0.1395233 4.674337 at 50iterations 6.1417978E-02 2.025484 at 60iterations 2.7004050E-02 0.8921337 at 70iterations 1.1942635E-02 0.3954887 at 80iterations 5.2708597E-03 0.1794949 at 90iterations 2.3313097E-03 8.7822437E-02 at 100iterations 1.0327073E-03 3.4927368E-02 at 110iterations 4.6049294E-04 1.5659332E-02 at 120iterations finished qdiffx linear iterations at : 07:01:29 total time elapsed so far: 7.220000 # loops : 120 mean,max change (kT/e) : 4.6049294E-04 1.5659332E-02 energy calculations done at 7.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.390000 DelPhi exited at 07:01:30 7.393u 0.214s 0:07.89 96.3% 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 Tue Oct 11 2011 at 07:01:30 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2962 !!! WARNING: UMP 317 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.601790 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): -60.28500 1.288000 ymin,ymax (A): -12.56500 41.05700 zmin,zma (A): 6.327000 54.74800 x,y,z range (A): 61.57300 53.62200 48.42100 scale (grids/A): 2.601790 object centre (A): -29.49850 14.24600 30.53750 number of atom coordinates read : 2962 total number of charged atoms : 2819 net assigned charge : -3.599983 assigned positive charge : 431.7266 centred at (gu) : 85.39856 84.18032 90.39481 assigned negative charge : -435.3271 centred at (gu) : 86.05957 85.12389 90.43063 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 165193 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26117 grid for indexing accessible points = 1.400000 m= 83205 mr = 118541 m= 28899 mr = 67610 m= 5824 mr = 22898 m= 555 mr = 4260 m= 9 mr = 292 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.260000 number of dielectric boundary points 70084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 22545 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) : 1.734527 object centre at (A) : -29.49850 14.24600 30.53750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1565857 0.2270623 midg,1,midg; midg,igrid,midg 0.1953858 -0.5210760 1,midg,midg; igrid,midg,midg -8.2194254E-02 -0.7380291 gauss-seidel spectral radius is 0.9992030 estimated iterations to convergence 280 setup time was (sec) 1.570000 now iterating at: 07:01:31 rms-change max change #iterations 9.312507 343.3820 at 10iterations 5.342734 115.6101 at 20iterations 3.038370 61.58075 at 30iterations 1.726311 37.22012 at 40iterations 0.9781782 20.65684 at 50iterations 0.5524645 11.01383 at 60iterations 0.3114970 6.555799 at 70iterations 0.1758928 3.499467 at 80iterations 9.9067725E-02 2.120843 at 90iterations 5.5732064E-02 1.135375 at 100iterations 3.1356119E-02 0.6065903 at 110iterations 1.7634897E-02 0.3679342 at 120iterations 9.9292547E-03 0.1999118 at 130iterations 5.5683092E-03 0.1045952 at 140iterations 3.1422586E-03 5.7210922E-02 at 150iterations 1.7632017E-03 3.4168243E-02 at 160iterations 9.9012628E-04 1.8302441E-02 at 170iterations 5.5776513E-04 1.0883331E-02 at 180iterations finished qdiffx linear iterations at : 07:01:42 total time elapsed so far: 11.78000 # loops : 180 mean,max change (kT/e) : 5.5776513E-04 1.0883331E-02 energy calculations done at 11.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.96000 DelPhi exited at 07:01:42 11.963u 0.218s 0:12.72 95.6% 0+0k 0+0io 0pf+0w