Tue Oct 11 08:16:29 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 08:16:29 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3621 !!! WARNING: HIZ 67 has a net charge of 0.2000 !!! WARNING: HIZ 170 has a net charge of 0.2000 !!! WARNING: HIZ 273 has a net charge of 0.2000 !!! WARNING: HIZ 682 has a net charge of 0.2000 !!! WARNING: HIZ 784 has a net charge of 0.2000 !!! WARNING: ZN1 1025 has a net charge of 1.4000 !!! WARNING: ZN1 1026 has a net charge of 1.4000 !!! WARNING: ZN1 1027 has a net charge of 1.4000 !!! WARNING: ZN1 1031 has a net charge of 1.4000 !!! WARNING: ZN1 1032 has a net charge of 1.4000 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: 0.4974707 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): -53.38400 -0.1880001 ymin,ymax (A): -38.38800 21.58600 zmin,zma (A): 11.19900 82.76100 x,y,z range (A): 53.19600 59.97400 71.56200 scale (grids/A): 0.4974707 object centre (A): -26.78600 -8.401000 46.98000 number of atom coordinates read : 3621 total number of charged atoms : 3454 net assigned charge : 8.000006 assigned positive charge : 551.1631 centred at (gu) : 88.17083 90.11847 91.38653 assigned negative charge : -543.1646 centred at (gu) : 88.34524 90.15668 91.37085 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5684 nv = 96 ne = 84 npr = 69292 no. pairs analyzed = 69292 no. exposed pairs = 5392 no. arc points = 38910 no. surface atoms = 1775 nbur = 1846 mkacc time = 0.2300000 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 = 1.708000 m= 197 mr = 2353 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 3529 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3764 ## 660 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 7800 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8489744E-11 1.0869529E-10 midg,1,midg; midg,igrid,midg 9.6664218E-11 1.5926512E-11 1,midg,midg; igrid,midg,midg 4.0541817E-10 -8.3854479E-11 gauss-seidel spectral radius is 0.9792769 estimated iterations to convergence 57 setup time was (sec) 0.8300000 now iterating at: 08:16:30 rms-change max change #iterations 5.4705147E-02 9.942493 at 10iterations 2.8295058E-03 0.4841747 at 20iterations 1.7211139E-04 3.0090332E-02 at 30iterations 2.0296206E-05 2.5444031E-03 at 40iterations 3.4354650E-06 3.5715103E-04 at 50iterations finished qdiffx linear iterations at : 08:16:34 total time elapsed so far: 4.530000 # loops : 50 mean,max change (kT/e) : 3.4354650E-06 3.5715103E-04 energy calculations done at 4.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.760000 DelPhi exited at 08:16:35 4.770u 0.472s 0:06.05 86.6% 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 08:16:35 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3621 !!! WARNING: HIZ 67 has a net charge of 0.2000 !!! WARNING: HIZ 170 has a net charge of 0.2000 !!! WARNING: HIZ 273 has a net charge of 0.2000 !!! WARNING: HIZ 682 has a net charge of 0.2000 !!! WARNING: HIZ 784 has a net charge of 0.2000 !!! WARNING: ZN1 1025 has a net charge of 1.4000 !!! WARNING: ZN1 1026 has a net charge of 1.4000 !!! WARNING: ZN1 1027 has a net charge of 1.4000 !!! WARNING: ZN1 1031 has a net charge of 1.4000 !!! WARNING: ZN1 1032 has a net charge of 1.4000 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: 1.492412 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): -53.38400 -0.1880001 ymin,ymax (A): -38.38800 21.58600 zmin,zma (A): 11.19900 82.76100 x,y,z range (A): 53.19600 59.97400 71.56200 scale (grids/A): 1.492412 object centre (A): -26.78600 -8.401000 46.98000 number of atom coordinates read : 3621 total number of charged atoms : 3454 net assigned charge : 8.000006 assigned positive charge : 551.1631 centred at (gu) : 84.51161 90.35470 94.15870 assigned negative charge : -543.1646 centred at (gu) : 85.03532 90.46957 94.11204 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 64012 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38910 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 15318 mr = 38570 m= 1027 mr = 8458 m= 19 mr = 235 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 99 time to turn everything in is 0.6800000 number of dielectric boundary points 33113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 561 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 25713 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) : 0.4974707 object centre at (A) : -26.78600 -8.401000 46.98000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1754827E-03 1.6855784E-02 midg,1,midg; midg,igrid,midg 1.2416014E-03 -6.4770216E-03 1,midg,midg; igrid,midg,midg 1.2564307E-02 -1.6110558E-03 gauss-seidel spectral radius is 0.9978963 estimated iterations to convergence 173 setup time was (sec) 1.020000 now iterating at: 08:16:36 rms-change max change #iterations 3.056801 166.4481 at 10iterations 1.176976 46.25529 at 20iterations 0.4589057 16.49996 at 30iterations 0.1775080 6.916546 at 40iterations 6.8760797E-02 2.802835 at 50iterations 2.6698487E-02 1.076935 at 60iterations 1.0319101E-02 0.4165878 at 70iterations 4.0347902E-03 0.1643600 at 80iterations 1.5711557E-03 6.1815262E-02 at 90iterations 6.1171316E-04 2.3021698E-02 at 100iterations 2.3916902E-04 9.9716187E-03 at 110iterations 9.3706178E-05 3.6163330E-03 at 120iterations finished qdiffx linear iterations at : 08:16:46 total time elapsed so far: 10.16000 # loops : 120 mean,max change (kT/e) : 9.3706178E-05 3.6163330E-03 energy calculations done at 10.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.38000 DelPhi exited at 08:16:46 10.386u 0.484s 0:11.16 97.3% 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 08:16:46 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3621 !!! WARNING: HIZ 67 has a net charge of 0.2000 !!! WARNING: HIZ 170 has a net charge of 0.2000 !!! WARNING: HIZ 273 has a net charge of 0.2000 !!! WARNING: HIZ 682 has a net charge of 0.2000 !!! WARNING: HIZ 784 has a net charge of 0.2000 !!! WARNING: ZN1 1025 has a net charge of 1.4000 !!! WARNING: ZN1 1026 has a net charge of 1.4000 !!! WARNING: ZN1 1027 has a net charge of 1.4000 !!! WARNING: ZN1 1031 has a net charge of 1.4000 !!! WARNING: ZN1 1032 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.238618 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): -53.38400 -0.1880001 ymin,ymax (A): -38.38800 21.58600 zmin,zma (A): 11.19900 82.76100 x,y,z range (A): 53.19600 59.97400 71.56200 scale (grids/A): 2.238618 object centre (A): -26.78600 -8.401000 46.98000 number of atom coordinates read : 3621 total number of charged atoms : 3454 net assigned charge : 8.000006 assigned positive charge : 551.1631 centred at (gu) : 81.76710 90.53166 96.23766 assigned negative charge : -543.1646 centred at (gu) : 82.55288 90.70417 96.16795 start vw surface at 0.1900000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 149325 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38910 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 56985 mr = 96611 m= 11520 mr = 40166 m= 1166 mr = 6790 m= 49 mr = 440 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 359 time to turn everything in is 1.620000 number of dielectric boundary points 75033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 87 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 27559 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) : 1.492412 object centre at (A) : -26.78600 -8.401000 46.98000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2345510E-03 0.2005393 midg,1,midg; midg,igrid,midg 1.9719781E-02 -0.1816482 1,midg,midg; igrid,midg,midg 0.1966465 -1.9561443E-02 gauss-seidel spectral radius is 0.9990702 estimated iterations to convergence 259 setup time was (sec) 1.990000 now iterating at: 08:16:49 rms-change max change #iterations 8.613966 276.8701 at 10iterations 4.870823 125.1340 at 20iterations 2.701809 72.82989 at 30iterations 1.487407 37.60899 at 40iterations 0.8151419 20.75573 at 50iterations 0.4434966 10.46085 at 60iterations 0.2411221 5.554501 at 70iterations 0.1305211 3.640112 at 80iterations 7.0459105E-02 1.796567 at 90iterations 3.8024366E-02 0.9250584 at 100iterations 2.0527918E-02 0.4853913 at 110iterations 1.1015038E-02 0.2581329 at 120iterations 5.9108469E-03 0.1414938 at 130iterations 3.1889449E-03 7.2217941E-02 at 140iterations 1.7093428E-03 4.0584564E-02 at 150iterations 9.1602537E-04 2.0475388E-02 at 160iterations 4.9212557E-04 1.0986328E-02 at 170iterations 2.6440294E-04 5.8946609E-03 at 180iterations finished qdiffx linear iterations at : 08:17:04 total time elapsed so far: 17.31000 # loops : 180 mean,max change (kT/e) : 2.6440294E-04 5.8946609E-03 energy calculations done at 17.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.53000 DelPhi exited at 08:17:05 17.533u 0.502s 0:18.45 97.7% 0+0k 0+0io 0pf+0w