Sun Oct 9 06:53:38 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 06:53:38 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1995 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6891212 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): -0.2689999 44.79000 ymin,ymax (A): -13.91900 34.49200 zmin,zma (A): -28.10600 23.55400 x,y,z range (A): 45.05900 48.41100 51.66000 scale (grids/A): 0.6891212 object centre (A): 22.26050 10.28650 -2.275999 number of atom coordinates read : 1995 total number of charged atoms : 1856 net assigned charge : -1.499990 assigned positive charge : 298.7900 centred at (gu) : 88.41035 90.57441 90.88094 assigned negative charge : -300.2901 centred at (gu) : 88.67332 90.61833 90.91818 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6424 nv = 96 ne = 84 npr = 42114 no. pairs analyzed = 42114 no. exposed pairs = 2481 no. arc points = 17558 no. surface atoms = 830 nbur = 1165 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 368 mr = 3602 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 128 time to turn everything in is 0.2600000 number of dielectric boundary points 3137 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1664 ## 140 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7260 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8972677E-09 -2.4932278E-08 midg,1,midg; midg,igrid,midg 3.8824672E-09 -2.5799872E-08 1,midg,midg; igrid,midg,midg 9.8261758E-08 -6.7858259E-08 gauss-seidel spectral radius is 0.9890237 estimated iterations to convergence 78 setup time was (sec) 0.5400000 now iterating at: 06:53:39 rms-change max change #iterations 0.1832039 26.47033 at 10iterations 2.1259135E-02 2.972710 at 20iterations 2.4612048E-03 0.3722801 at 30iterations 2.9174966E-04 4.4515610E-02 at 40iterations 3.3590608E-05 4.8370361E-03 at 50iterations finished qdiffx linear iterations at : 06:53:43 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 3.3590608E-05 4.8370361E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 06:53:43 4.216u 0.249s 0:04.73 94.0% 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 06:53:43 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 = 1995 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 2.067364 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): -0.2689999 44.79000 ymin,ymax (A): -13.91900 34.49200 zmin,zma (A): -28.10600 23.55400 x,y,z range (A): 45.05900 48.41100 51.66000 scale (grids/A): 2.067364 object centre (A): 22.26050 10.28650 -2.275999 number of atom coordinates read : 1995 total number of charged atoms : 1856 net assigned charge : -1.499990 assigned positive charge : 298.7900 centred at (gu) : 85.23089 91.72304 92.64294 assigned negative charge : -300.2901 centred at (gu) : 86.01998 91.85503 92.75456 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 68419 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17558 grid for indexing accessible points = 1.400000 m= 25092 mr = 47529 m= 4367 mr = 18780 m= 318 mr = 2898 m= 5 mr = 155 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 2862 time to turn everything in is 0.5700000 number of dielectric boundary points 28839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 14728 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) : 0.6891212 object centre at (A) : 22.26050 10.28650 -2.275999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9189978E-02 -4.9071640E-02 midg,1,midg; midg,igrid,midg -3.7449956E-02 -2.9215880E-02 1,midg,midg; igrid,midg,midg 8.2665376E-02 -3.5187218E-02 gauss-seidel spectral radius is 0.9987690 estimated iterations to convergence 226 setup time was (sec) 0.9200000 now iterating at: 06:53:44 rms-change max change #iterations 4.366079 199.7279 at 10iterations 2.110915 87.14679 at 20iterations 1.028773 31.94230 at 30iterations 0.5005831 16.81477 at 40iterations 0.2440660 7.607562 at 50iterations 0.1190508 3.765218 at 60iterations 5.7688035E-02 1.882462 at 70iterations 2.8046001E-02 0.9612522 at 80iterations 1.3711120E-02 0.4308891 at 90iterations 6.6301632E-03 0.2107971 at 100iterations 3.2227731E-03 0.1038651 at 110iterations 1.5722293E-03 5.0471604E-02 at 120iterations finished qdiffx linear iterations at : 06:53:53 total time elapsed so far: 9.680000 # loops : 120 mean,max change (kT/e) : 1.5722293E-03 5.0471604E-02 energy calculations done at 9.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.870000 DelPhi exited at 06:53:54 9.869u 0.326s 0:10.48 97.1% 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 Sun Oct 9 2011 at 06:53:54 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 = 1995 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.101045 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): -0.2689999 44.79000 ymin,ymax (A): -13.91900 34.49200 zmin,zma (A): -28.10600 23.55400 x,y,z range (A): 45.05900 48.41100 51.66000 scale (grids/A): 3.101045 object centre (A): 22.26050 10.28650 -2.275999 number of atom coordinates read : 1995 total number of charged atoms : 1856 net assigned charge : -1.499990 assigned positive charge : 298.7900 centred at (gu) : 82.84645 92.58475 93.96436 assigned negative charge : -300.2901 centred at (gu) : 84.03004 92.78258 94.13184 start vw surface at 0.1300000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 157936 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17558 grid for indexing accessible points = 1.400000 m= 80715 mr = 114792 m= 30441 mr = 66704 m= 8206 mr = 24848 m= 1377 mr = 6370 m= 129 mr = 960 m= 1 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 9693 time to turn everything in is 1.780000 number of dielectric boundary points 65059 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 14848 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) : 2.067364 object centre at (A) : 22.26050 10.28650 -2.275999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5362846 -0.5689824 midg,1,midg; midg,igrid,midg -0.5411446 -0.4295905 1,midg,midg; igrid,midg,midg 0.9965044 -0.2769190 gauss-seidel spectral radius is 0.9992833 estimated iterations to convergence 295 setup time was (sec) 2.130000 now iterating at: 06:53:56 rms-change max change #iterations 9.837537 422.9426 at 10iterations 5.703862 133.0636 at 20iterations 3.308031 63.22677 at 30iterations 1.916535 35.63539 at 40iterations 1.111124 21.17219 at 50iterations 0.6430566 11.91640 at 60iterations 0.3727238 7.383279 at 70iterations 0.2157800 4.514282 at 80iterations 0.1246540 2.324627 at 90iterations 7.2103240E-02 1.398692 at 100iterations 4.1737407E-02 0.7525620 at 110iterations 2.4195716E-02 0.4228401 at 120iterations 1.4010279E-02 0.2512474 at 130iterations 8.0728391E-03 0.1372528 at 140iterations 4.6868888E-03 8.3137512E-02 at 150iterations 2.7090074E-03 4.6298981E-02 at 160iterations 1.5662950E-03 2.7752876E-02 at 170iterations 9.0863707E-04 1.6359329E-02 at 180iterations finished qdiffx linear iterations at : 06:54:10 total time elapsed so far: 16.40000 # loops : 180 mean,max change (kT/e) : 9.0863707E-04 1.6359329E-02 energy calculations done at 16.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.59000 DelPhi exited at 06:54:11 16.590u 0.323s 0:17.19 98.3% 0+0k 0+0io 0pf+0w