Tue Oct 11 03:26:19 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 03:26:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3526 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: 0.5418403 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): 45.89000 101.4730 ymin,ymax (A): -1.288000 61.12100 zmin,zma (A): 56.37300 122.0750 x,y,z range (A): 55.58300 62.40900 65.70201 scale (grids/A): 0.5418403 object centre (A): 73.68150 29.91650 89.22400 number of atom coordinates read : 3526 total number of charged atoms : 3373 net assigned charge : 4.000026 assigned positive charge : 546.2081 centred at (gu) : 88.67425 89.92756 88.11447 assigned negative charge : -542.2100 centred at (gu) : 88.74827 89.98808 88.16154 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6635 nv = 96 ne = 84 npr = 68672 no. pairs analyzed = 68672 no. exposed pairs = 4920 no. arc points = 34549 no. surface atoms = 1624 nbur = 1902 mkacc time = 0.1200000 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 = 1.596000 m= 260 mr = 3128 m= 0 mr = 4 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2300000 number of dielectric boundary points 3763 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3461 ## 493 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8818 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3299928E-10 -7.8578519E-11 midg,1,midg; midg,igrid,midg 6.2086480E-10 -2.2042403E-10 1,midg,midg; igrid,midg,midg 9.7935704E-10 -2.2639565E-10 gauss-seidel spectral radius is 0.9824902 estimated iterations to convergence 62 setup time was (sec) 0.4200000 now iterating at: 03:26:20 rms-change max change #iterations 7.8038372E-02 11.53156 at 10iterations 4.9626664E-03 0.7551003 at 20iterations 3.3675088E-04 4.9613953E-02 at 30iterations 2.3774608E-05 4.1618347E-03 at 40iterations 3.0998858E-06 6.0033798E-04 at 50iterations finished qdiffx linear iterations at : 03:26:23 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 3.0998858E-06 6.0033798E-04 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 03:26:23 3.383u 0.177s 0:03.91 90.7% 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 03:26:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3526 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: 1.625521 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): 45.89000 101.4730 ymin,ymax (A): -1.288000 61.12100 zmin,zma (A): 56.37300 122.0750 x,y,z range (A): 55.58300 62.40900 65.70201 scale (grids/A): 1.625521 object centre (A): 73.68150 29.91650 89.22400 number of atom coordinates read : 3526 total number of charged atoms : 3373 net assigned charge : 4.000026 assigned positive charge : 546.2081 centred at (gu) : 86.02163 89.78171 84.34258 assigned negative charge : -542.2100 centred at (gu) : 86.24424 89.96407 84.48409 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 72761 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34549 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21637 mr = 46455 m= 2280 mr = 14260 m= 50 mr = 1066 m= 0 mr = 1 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 375 time to turn everything in is 0.3700000 number of dielectric boundary points 34946 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 450 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 25810 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) : 0.5418403 object centre at (A) : 73.68150 29.91650 89.22400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0061536E-02 -2.2749802E-04 midg,1,midg; midg,igrid,midg -4.5868703E-03 -1.2924749E-02 1,midg,midg; igrid,midg,midg 1.3671417E-02 2.4726088E-03 gauss-seidel spectral radius is 0.9982327 estimated iterations to convergence 189 setup time was (sec) 0.6000000 now iterating at: 03:26:24 rms-change max change #iterations 3.675565 181.5863 at 10iterations 1.533478 55.51797 at 20iterations 0.6469396 25.12226 at 30iterations 0.2712650 9.570002 at 40iterations 0.1143009 3.754203 at 50iterations 4.7879454E-02 1.761929 at 60iterations 2.0220494E-02 0.7083974 at 70iterations 8.5160099E-03 0.3354568 at 80iterations 3.5839351E-03 0.1382141 at 90iterations 1.5162535E-03 5.3066254E-02 at 100iterations 6.4100418E-04 2.1977901E-02 at 110iterations 2.6966407E-04 9.1643333E-03 at 120iterations finished qdiffx linear iterations at : 03:26:31 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 2.6966407E-04 9.1643333E-03 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 03:26:32 7.950u 0.183s 0:08.61 94.4% 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 Tue Oct 11 2011 at 03:26:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3526 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: 2.438282 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): 45.89000 101.4730 ymin,ymax (A): -1.288000 61.12100 zmin,zma (A): 56.37300 122.0750 x,y,z range (A): 55.58300 62.40900 65.70201 scale (grids/A): 2.438282 object centre (A): 73.68150 29.91650 89.22400 number of atom coordinates read : 3526 total number of charged atoms : 3373 net assigned charge : 4.000026 assigned positive charge : 546.2081 centred at (gu) : 84.03221 89.67222 81.51378 assigned negative charge : -542.2100 centred at (gu) : 84.36637 89.94580 81.72602 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 168453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34549 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 74441 mr = 114180 m= 21181 mr = 56734 m= 3497 mr = 15538 m= 239 mr = 2282 m= 8 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 1407 time to turn everything in is 0.8900000 number of dielectric boundary points 78987 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 26950 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) : 1.625521 object centre at (A) : 73.68150 29.91650 89.22400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5385011E-03 8.6765453E-02 midg,1,midg; midg,igrid,midg -8.2268544E-02 -0.1991249 1,midg,midg; igrid,midg,midg 0.1969224 3.9951880E-02 gauss-seidel spectral radius is 0.9991691 estimated iterations to convergence 274 setup time was (sec) 1.130000 now iterating at: 03:26:33 rms-change max change #iterations 9.684238 379.7158 at 10iterations 5.569283 143.0617 at 20iterations 3.169176 71.39088 at 30iterations 1.797088 41.55976 at 40iterations 1.014898 22.12035 at 50iterations 0.5705809 12.14461 at 60iterations 0.3197603 6.752483 at 70iterations 0.1794210 3.898884 at 80iterations 0.1001989 1.956724 at 90iterations 5.5822454E-02 1.111924 at 100iterations 3.1223448E-02 0.6158280 at 110iterations 1.7348330E-02 0.3738185 at 120iterations 9.6648792E-03 0.1960144 at 130iterations 5.3870436E-03 0.1313803 at 140iterations 3.0028338E-03 5.9364319E-02 at 150iterations 1.6708345E-03 3.6777496E-02 at 160iterations 9.2842506E-04 2.1751404E-02 at 170iterations 5.1712181E-04 1.0908127E-02 at 180iterations finished qdiffx linear iterations at : 03:26:45 total time elapsed so far: 12.53000 # loops : 180 mean,max change (kT/e) : 5.1712181E-04 1.0908127E-02 energy calculations done at 12.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.66000 DelPhi exited at 03:26:45 12.666u 0.195s 0:13.41 95.8% 0+0k 0+0io 0pf+0w