Sat Oct 8 14:53:40 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 Sat Oct 8 2011 at 14:53:40 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2990 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6408064 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): -12.22200 43.33300 ymin,ymax (A): -23.98200 22.74500 zmin,zma (A): -7.615000 47.31300 x,y,z range (A): 55.55500 46.72700 54.92800 scale (grids/A): 0.6408064 object centre (A): 15.55550 -0.6185007 19.84900 number of atom coordinates read : 2990 total number of charged atoms : 2845 net assigned charge : 1.228008 assigned positive charge : 447.4886 centred at (gu) : 88.76820 90.03761 91.82387 assigned negative charge : -446.2614 centred at (gu) : 88.70753 89.89374 91.81676 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8075 nv = 96 ne = 84 npr = 63004 no. pairs analyzed = 63004 no. exposed pairs = 3347 no. arc points = 23620 no. surface atoms = 1144 nbur = 1846 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 392 mr = 4733 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3692 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2222 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9817 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7024625E-10 4.2665649E-09 midg,1,midg; midg,igrid,midg -1.7858691E-08 2.1413477E-08 1,midg,midg; igrid,midg,midg -8.4312006E-09 7.7909323E-09 gauss-seidel spectral radius is 0.9874108 estimated iterations to convergence 73 setup time was (sec) 0.6600000 now iterating at: 14:53:41 rms-change max change #iterations 0.1608088 20.61341 at 10iterations 1.6166858E-02 2.358972 at 20iterations 1.6602835E-03 0.2075424 at 30iterations 1.9050935E-04 3.1318665E-02 at 40iterations 2.4614252E-05 3.2043457E-03 at 50iterations finished qdiffx linear iterations at : 14:53:44 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 2.4614252E-05 3.2043457E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 14:53:44 4.113u 0.264s 0:04.69 93.1% 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 Sat Oct 8 2011 at 14:53:44 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2990 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.922419 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): -12.22200 43.33300 ymin,ymax (A): -23.98200 22.74500 zmin,zma (A): -7.615000 47.31300 x,y,z range (A): 55.55500 46.72700 54.92800 scale (grids/A): 1.922419 object centre (A): 15.55550 -0.6185007 19.84900 number of atom coordinates read : 2990 total number of charged atoms : 2845 net assigned charge : 1.228008 assigned positive charge : 447.4886 centred at (gu) : 86.30388 90.11250 95.47091 assigned negative charge : -446.2614 centred at (gu) : 86.12241 89.68091 95.44982 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 88238 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23620 grid for indexing accessible points = 1.400000 m= 31242 mr = 63621 m= 4593 mr = 23555 m= 302 mr = 2837 m= 1 mr = 113 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 0.7500000 number of dielectric boundary points 34250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 163 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 22404 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) : 0.6408064 object centre at (A) : 15.55550 -0.6185007 19.84900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3527836E-02 6.3075353E-03 midg,1,midg; midg,igrid,midg -1.7230026E-04 2.9447472E-02 1,midg,midg; igrid,midg,midg -3.4873873E-02 1.2124670E-02 gauss-seidel spectral radius is 0.9986882 estimated iterations to convergence 219 setup time was (sec) 1.050000 now iterating at: 14:53:46 rms-change max change #iterations 4.683431 266.0701 at 10iterations 2.238923 72.03137 at 20iterations 1.065754 32.26721 at 30iterations 0.5066261 14.07388 at 40iterations 0.2416323 7.431108 at 50iterations 0.1150558 3.328884 at 60iterations 5.4808788E-02 1.627764 at 70iterations 2.6084600E-02 0.7423320 at 80iterations 1.2425016E-02 0.3597202 at 90iterations 5.9278174E-03 0.1563058 at 100iterations 2.8160436E-03 8.7153435E-02 at 110iterations 1.3455529E-03 3.8711548E-02 at 120iterations finished qdiffx linear iterations at : 14:53:54 total time elapsed so far: 9.380000 # loops : 120 mean,max change (kT/e) : 1.3455529E-03 3.8711548E-02 energy calculations done at 9.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.550000 DelPhi exited at 14:53:55 9.555u 0.300s 0:10.23 96.2% 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 Sat Oct 8 2011 at 14:53:55 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2990 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.883629 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): -12.22200 43.33300 ymin,ymax (A): -23.98200 22.74500 zmin,zma (A): -7.615000 47.31300 x,y,z range (A): 55.55500 46.72700 54.92800 scale (grids/A): 2.883629 object centre (A): 15.55550 -0.6185007 19.84900 number of atom coordinates read : 2990 total number of charged atoms : 2845 net assigned charge : 1.228008 assigned positive charge : 447.4886 centred at (gu) : 84.45558 90.16831 98.20638 assigned negative charge : -446.2614 centred at (gu) : 84.18349 89.52126 98.17469 start vw surface at 0.1600000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 204325 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23620 grid for indexing accessible points = 1.400000 m= 103013 mr = 153604 m= 35677 mr = 85895 m= 8207 mr = 28838 m= 1210 mr = 6086 m= 64 mr = 803 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.970000 number of dielectric boundary points 77243 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.130000 number of grid points assigned charge 22759 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) : 1.922419 object centre at (A) : 15.55550 -0.6185007 19.84900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8337281E-02 0.2211516 midg,1,midg; midg,igrid,midg -6.4474149E-03 0.3315880 1,midg,midg; igrid,midg,midg -0.4306731 0.1756569 gauss-seidel spectral radius is 0.9992761 estimated iterations to convergence 293 setup time was (sec) 2.300000 now iterating at: 14:53:57 rms-change max change #iterations 10.83738 382.2507 at 10iterations 6.339873 136.6075 at 20iterations 3.690826 73.96610 at 30iterations 2.143886 43.41103 at 40iterations 1.241424 20.57693 at 50iterations 0.7210512 13.81041 at 60iterations 0.4169667 6.800661 at 70iterations 0.2413753 4.223572 at 80iterations 0.1395710 2.388412 at 90iterations 8.0761001E-02 1.324451 at 100iterations 4.6722785E-02 0.7620087 at 110iterations 2.7013062E-02 0.4702148 at 120iterations 1.5630120E-02 0.2546120 at 130iterations 9.0460526E-03 0.1533203 at 140iterations 5.2266433E-03 9.3309402E-02 at 150iterations 3.0229827E-03 4.9716949E-02 at 160iterations 1.7533175E-03 3.1947136E-02 at 170iterations 1.0178179E-03 1.7646790E-02 at 180iterations finished qdiffx linear iterations at : 14:54:11 total time elapsed so far: 16.00000 # loops : 180 mean,max change (kT/e) : 1.0178179E-03 1.7646790E-02 energy calculations done at 16.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.18000 DelPhi exited at 14:54:12 16.186u 0.304s 0:16.78 98.2% 0+0k 0+0io 0pf+0w