Tue Oct 11 08:24:59 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 08:24:59 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3141 !!! WARNING: HIR 58 has a net charge of 0.5140 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: 0.6076330 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): -20.64800 31.02100 ymin,ymax (A): -15.47700 36.34500 zmin,zma (A): -24.05900 34.52900 x,y,z range (A): 51.66900 51.82200 58.58800 scale (grids/A): 0.6076330 object centre (A): 5.186501 10.43400 5.235000 number of atom coordinates read : 3141 total number of charged atoms : 3003 net assigned charge : -6.485977 assigned positive charge : 470.2758 centred at (gu) : 91.23437 89.98851 91.57847 assigned negative charge : -476.7630 centred at (gu) : 91.24315 90.06956 91.58068 start vw surface at 0.2100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7841 nv = 96 ne = 84 npr = 63818 no. pairs analyzed = 63818 no. exposed pairs = 3939 no. arc points = 27242 no. surface atoms = 1344 nbur = 1797 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 4312 m= 3 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 3899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2842 ## 305 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 9752 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4254350E-09 -5.1620463E-09 midg,1,midg; midg,igrid,midg 1.0031124E-09 -8.1175129E-09 1,midg,midg; igrid,midg,midg -2.3302709E-09 -5.2767866E-09 gauss-seidel spectral radius is 0.9860277 estimated iterations to convergence 69 setup time was (sec) 0.7300000 now iterating at: 08:25:00 rms-change max change #iterations 0.1270039 20.90494 at 10iterations 1.1424252E-02 1.698192 at 20iterations 1.3369138E-03 0.1933036 at 30iterations 3.3567814E-04 5.3041458E-02 at 40iterations 1.1925358E-04 1.7494202E-02 at 50iterations finished qdiffx linear iterations at : 08:25:03 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 1.1925358E-04 1.7494202E-02 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 08:25:04 4.194u 0.188s 0:04.70 92.9% 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 08:25:04 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3141 !!! WARNING: HIR 58 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.822899 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): -20.64800 31.02100 ymin,ymax (A): -15.47700 36.34500 zmin,zma (A): -24.05900 34.52900 x,y,z range (A): 51.66900 51.82200 58.58800 scale (grids/A): 1.822899 object centre (A): 5.186501 10.43400 5.235000 number of atom coordinates read : 3141 total number of charged atoms : 3003 net assigned charge : -6.485977 assigned positive charge : 470.2758 centred at (gu) : 93.70242 89.96470 94.73463 assigned negative charge : -476.7630 centred at (gu) : 93.72920 90.20782 94.74145 start vw surface at 0.1900000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 85414 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27242 grid for indexing accessible points = 1.400000 m= 30528 mr = 59627 m= 4022 mr = 22331 m= 155 mr = 2275 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7700000 number of dielectric boundary points 35859 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 261 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 23497 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) : 0.6076330 object centre at (A) : 5.186501 10.43400 5.235000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2870444E-02 -3.8172573E-02 midg,1,midg; midg,igrid,midg -1.8792456E-03 -2.4698285E-02 1,midg,midg; igrid,midg,midg -6.6800802E-03 -1.6392843E-03 gauss-seidel spectral radius is 0.9985681 estimated iterations to convergence 210 setup time was (sec) 1.120000 now iterating at: 08:25:05 rms-change max change #iterations 4.327590 189.0247 at 10iterations 1.972551 59.70052 at 20iterations 0.9094900 28.41202 at 30iterations 0.4178143 11.94436 at 40iterations 0.1926746 6.459023 at 50iterations 8.8496543E-02 2.604891 at 60iterations 4.0804535E-02 1.183980 at 70iterations 1.8871481E-02 0.6343956 at 80iterations 8.7467274E-03 0.2995377 at 90iterations 4.0971991E-03 0.1318207 at 100iterations 1.9791652E-03 6.2583923E-02 at 110iterations 1.0049739E-03 3.1091690E-02 at 120iterations finished qdiffx linear iterations at : 08:25:13 total time elapsed so far: 9.470000 # loops : 120 mean,max change (kT/e) : 1.0049739E-03 3.1091690E-02 energy calculations done at 9.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.710000 DelPhi exited at 08:25:14 9.710u 0.244s 0:10.37 95.9% 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 08:25:14 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3141 !!! WARNING: HIR 58 has a net charge of 0.5140 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: 2.734349 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): -20.64800 31.02100 ymin,ymax (A): -15.47700 36.34500 zmin,zma (A): -24.05900 34.52900 x,y,z range (A): 51.66900 51.82200 58.58800 scale (grids/A): 2.734349 object centre (A): 5.186501 10.43400 5.235000 number of atom coordinates read : 3141 total number of charged atoms : 3003 net assigned charge : -6.485977 assigned positive charge : 470.2758 centred at (gu) : 95.55338 89.94677 97.10166 assigned negative charge : -476.7630 centred at (gu) : 95.59349 90.31161 97.11200 start vw surface at 0.2100000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 197448 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27242 grid for indexing accessible points = 1.400000 m= 100826 mr = 144327 m= 34059 mr = 82545 m= 6933 mr = 27007 m= 662 mr = 4798 m= 26 mr = 353 m= 0 mr = 7 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.000000 number of dielectric boundary points 80917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 2.170000 number of grid points assigned charge 24020 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) : 1.822899 object centre at (A) : 5.186501 10.43400 5.235000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3895146E-02 -0.4147362 midg,1,midg; midg,igrid,midg -3.3750266E-02 -0.2567398 1,midg,midg; igrid,midg,midg -0.1237759 -5.2479159E-02 gauss-seidel spectral radius is 0.9992570 estimated iterations to convergence 290 setup time was (sec) 2.380000 now iterating at: 08:25:17 rms-change max change #iterations 10.36381 434.4482 at 10iterations 6.077350 141.8438 at 20iterations 3.535270 67.37038 at 30iterations 2.048175 37.94926 at 40iterations 1.185155 26.31093 at 50iterations 0.6825075 14.19855 at 60iterations 0.3945657 7.380383 at 70iterations 0.2268828 3.963367 at 80iterations 0.1304347 2.342657 at 90iterations 7.5265706E-02 1.363574 at 100iterations 4.3253005E-02 0.7518425 at 110iterations 2.4901396E-02 0.5143394 at 120iterations 1.4333289E-02 0.2353902 at 130iterations 8.2916990E-03 0.1413498 at 140iterations 4.8308549E-03 8.3896637E-02 at 150iterations 2.8329494E-03 5.6504250E-02 at 160iterations 1.7022274E-03 3.4193039E-02 at 170iterations 1.0594223E-03 2.0562291E-02 at 180iterations finished qdiffx linear iterations at : 08:25:30 total time elapsed so far: 15.97000 # loops : 180 mean,max change (kT/e) : 1.0594223E-03 2.0562291E-02 energy calculations done at 15.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.20000 DelPhi exited at 08:25:31 16.200u 0.256s 0:16.84 97.6% 0+0k 0+0io 0pf+0w