Sat Oct 8 18:25:42 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 Sat Oct 8 2011 at 18:25:42 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3377 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: 0.5726879 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): -27.00100 24.75300 ymin,ymax (A): 18.23500 80.39800 zmin,zma (A): -11.99500 43.07700 x,y,z range (A): 51.75400 62.16300 55.07200 scale (grids/A): 0.5726879 object centre (A): -1.124000 49.31650 15.54100 number of atom coordinates read : 3377 total number of charged atoms : 3232 net assigned charge : 8.500029 assigned positive charge : 516.4724 centred at (gu) : 91.24651 88.74199 89.01527 assigned negative charge : -507.9738 centred at (gu) : 91.23538 88.80032 88.95676 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7477 nv = 96 ne = 84 npr = 65615 no. pairs analyzed = 65615 no. exposed pairs = 4711 no. arc points = 33834 no. surface atoms = 1539 nbur = 1838 mkacc time = 0.1100000 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 = 1.512000 m= 373 mr = 3704 m= 3 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2400000 number of dielectric boundary points 4122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3351 ## 419 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9490 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1962891E-10 2.0360933E-09 midg,1,midg; midg,igrid,midg 3.4440157E-09 2.1700997E-10 1,midg,midg; igrid,midg,midg 9.0957752E-10 2.1928197E-09 gauss-seidel spectral radius is 0.9843102 estimated iterations to convergence 66 setup time was (sec) 0.4400000 now iterating at: 18:25:43 rms-change max change #iterations 0.1017951 15.09980 at 10iterations 9.1438107E-03 1.451279 at 20iterations 1.9379400E-03 0.3685265 at 30iterations 7.1407267E-04 0.1366920 at 40iterations 2.7422362E-04 5.2528381E-02 at 50iterations finished qdiffx linear iterations at : 18:25:46 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 2.7422362E-04 5.2528381E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 18:25:46 3.403u 0.155s 0:03.84 92.4% 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 18:25:46 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3377 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: 1.718064 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): -27.00100 24.75300 ymin,ymax (A): 18.23500 80.39800 zmin,zma (A): -11.99500 43.07700 x,y,z range (A): 51.75400 62.16300 55.07200 scale (grids/A): 1.718064 object centre (A): -1.124000 49.31650 15.54100 number of atom coordinates read : 3377 total number of charged atoms : 3232 net assigned charge : 8.500029 assigned positive charge : 516.4724 centred at (gu) : 93.73856 86.22524 87.04484 assigned negative charge : -507.9738 centred at (gu) : 93.70580 86.40056 86.86986 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80996 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33834 grid for indexing accessible points = 1.400000 m= 27840 mr = 53140 m= 3804 mr = 19106 m= 144 mr = 2006 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 927 time to turn everything in is 0.4000000 number of dielectric boundary points 38519 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 338 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 25036 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) : 0.5726879 object centre at (A) : -1.124000 49.31650 15.54100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1186953E-03 9.6329385E-03 midg,1,midg; midg,igrid,midg 3.3579808E-02 4.5951270E-03 1,midg,midg; igrid,midg,midg 5.2096583E-03 1.3321795E-02 gauss-seidel spectral radius is 0.9984206 estimated iterations to convergence 200 setup time was (sec) 0.6100000 now iterating at: 18:25:47 rms-change max change #iterations 4.007874 161.9210 at 10iterations 1.758296 75.29929 at 20iterations 0.7769915 24.86017 at 30iterations 0.3441264 11.57424 at 40iterations 0.1518634 5.018562 at 50iterations 6.7460433E-02 2.285679 at 60iterations 3.0145727E-02 1.006912 at 70iterations 1.3762563E-02 0.4898224 at 80iterations 6.5965410E-03 0.2493973 at 90iterations 3.4590142E-03 0.1422424 at 100iterations 2.0072905E-03 7.7682495E-02 at 110iterations 1.2949118E-03 5.0498962E-02 at 120iterations finished qdiffx linear iterations at : 18:25:54 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 1.2949118E-03 5.0498962E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 18:25:55 7.773u 0.185s 0:08.27 96.1% 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 18:25:55 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3377 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: 2.577096 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): -27.00100 24.75300 ymin,ymax (A): 18.23500 80.39800 zmin,zma (A): -11.99500 43.07700 x,y,z range (A): 51.75400 62.16300 55.07200 scale (grids/A): 2.577096 object centre (A): -1.124000 49.31650 15.54100 number of atom coordinates read : 3377 total number of charged atoms : 3232 net assigned charge : 8.500029 assigned positive charge : 516.4724 centred at (gu) : 95.60757 84.33754 85.56715 assigned negative charge : -507.9738 centred at (gu) : 95.55846 84.60065 85.30469 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 187480 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33834 grid for indexing accessible points = 1.400000 m= 91246 mr = 130389 m= 30984 mr = 71240 m= 6274 mr = 23534 m= 545 mr = 4089 m= 26 mr = 237 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 2899 time to turn everything in is 0.9900000 number of dielectric boundary points 87061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 25844 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) : 1.718064 object centre at (A) : -1.124000 49.31650 15.54100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0129295E-02 0.1156033 midg,1,midg; midg,igrid,midg 0.3773050 4.4424828E-02 1,midg,midg; igrid,midg,midg 5.5153176E-02 0.1726878 gauss-seidel spectral radius is 0.9992249 estimated iterations to convergence 284 setup time was (sec) 1.230000 now iterating at: 18:25:56 rms-change max change #iterations 10.26392 346.5390 at 10iterations 6.037532 154.9740 at 20iterations 3.514339 84.92818 at 30iterations 2.032980 44.49579 at 40iterations 1.174086 26.66863 at 50iterations 0.6743447 15.10327 at 60iterations 0.3858807 7.095425 at 70iterations 0.2203588 4.776344 at 80iterations 0.1261052 2.898407 at 90iterations 7.1883939E-02 1.399746 at 100iterations 4.0888663E-02 0.7376862 at 110iterations 2.3363773E-02 0.4893646 at 120iterations 1.3344395E-02 0.2662926 at 130iterations 7.6553440E-03 0.1779938 at 140iterations 4.4291159E-03 8.6723328E-02 at 150iterations 2.6092057E-03 5.1429749E-02 at 160iterations 1.5815882E-03 3.4358978E-02 at 170iterations 1.0057677E-03 2.2891998E-02 at 180iterations finished qdiffx linear iterations at : 18:26:07 total time elapsed so far: 12.59000 # loops : 180 mean,max change (kT/e) : 1.0057677E-03 2.2891998E-02 energy calculations done at 12.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 18:26:08 12.708u 0.215s 0:13.21 97.7% 0+0k 0+0io 0pf+0w