Sat Nov 19 11:31:33 PST 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 Nov 19 2011 at 11:31:34 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 ! Automatically converted by prot2crg.py # of charge parameter records: 950 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3338 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: DIC 295 has a net charge of -0.8000 !!! WARNING: ZN 522 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6327539 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): 31.96600 81.47400 ymin,ymax (A): 25.28900 81.55100 zmin,zma (A): -2.859000 46.34600 x,y,z range (A): 49.50800 56.26200 49.20500 scale (grids/A): 0.6327539 object centre (A): 56.72000 53.42000 21.74350 number of atom coordinates read : 3338 total number of charged atoms : 3187 net assigned charge : -6.999975 assigned positive charge : 508.5882 centred at (gu) : 90.88586 89.62329 91.06296 assigned negative charge : -515.5894 centred at (gu) : 90.66769 89.71857 91.00449 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8715 nv = 96 ne = 84 npr = 70816 no. pairs analyzed = 70816 no. exposed pairs = 3582 no. arc points = 24533 no. surface atoms = 1230 nbur = 2108 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 491 mr = 5390 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3000000 number of dielectric boundary points 3765 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2436 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 10714 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2816052E-08 -1.4521440E-09 midg,1,midg; midg,igrid,midg 3.6669356E-09 -1.9198625E-08 1,midg,midg; igrid,midg,midg -3.0490057E-08 2.2479268E-08 gauss-seidel spectral radius is 0.9871128 estimated iterations to convergence 72 setup time was (sec) 0.5100000 now iterating at: 11:31:35 rms-change max change #iterations 0.1620555 22.94128 at 10iterations 1.6013904E-02 2.229889 at 20iterations 1.5405340E-03 0.1939220 at 30iterations 1.5687758E-04 1.9962311E-02 at 40iterations 1.5619815E-05 2.0790100E-03 at 50iterations finished qdiffx linear iterations at : 11:31:38 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 1.5619815E-05 2.0790100E-03 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 11:31:38 3.593u 0.181s 0:04.55 82.8% 0+0k 0+45968io 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 Nov 19 2011 at 11:31:38 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 ! Automatically converted by prot2crg.py # of charge parameter records: 950 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3338 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: DIC 295 has a net charge of -0.8000 !!! WARNING: ZN 522 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.898262 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): 31.96600 81.47400 ymin,ymax (A): 25.28900 81.55100 zmin,zma (A): -2.859000 46.34600 x,y,z range (A): 49.50800 56.26200 49.20500 scale (grids/A): 1.898262 object centre (A): 56.72000 53.42000 21.74350 number of atom coordinates read : 3338 total number of charged atoms : 3187 net assigned charge : -6.999975 assigned positive charge : 508.5882 centred at (gu) : 92.65668 88.86913 93.18771 assigned negative charge : -515.5894 centred at (gu) : 92.00230 89.15504 93.01288 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 94752 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24533 grid for indexing accessible points = 1.400000 m= 37061 mr = 69848 m= 6181 mr = 29376 m= 343 mr = 4307 m= 2 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 2636 time to turn everything in is 0.5800000 number of dielectric boundary points 34673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 25071 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) : 0.6327539 object centre at (A) : 56.72000 53.42000 21.74350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6175564E-02 -2.6485329E-02 midg,1,midg; midg,igrid,midg -9.0928823E-03 -4.0340398E-02 1,midg,midg; igrid,midg,midg -4.5258395E-02 2.0911468E-02 gauss-seidel spectral radius is 0.9986803 estimated iterations to convergence 218 setup time was (sec) 0.7900000 now iterating at: 11:31:39 rms-change max change #iterations 4.932659 178.7165 at 10iterations 2.344446 74.15729 at 20iterations 1.114637 30.89028 at 30iterations 0.5304209 16.27540 at 40iterations 0.2517556 6.848141 at 50iterations 0.1200287 3.252759 at 60iterations 5.6794778E-02 1.548580 at 70iterations 2.7003990E-02 0.7319260 at 80iterations 1.2810695E-02 0.3558807 at 90iterations 6.1051561E-03 0.1672211 at 100iterations 2.9025988E-03 8.0780029E-02 at 110iterations 1.3812897E-03 3.6000967E-02 at 120iterations finished qdiffx linear iterations at : 11:31:47 total time elapsed so far: 8.100000 # loops : 120 mean,max change (kT/e) : 1.3812897E-03 3.6000967E-02 energy calculations done at 8.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.240000 DelPhi exited at 11:31:47 8.245u 0.209s 0:08.85 95.3% 0+0k 0+45368io 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 Nov 19 2011 at 11:31:47 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 ! Automatically converted by prot2crg.py # of charge parameter records: 950 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3338 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: DIC 295 has a net charge of -0.8000 !!! WARNING: ZN 522 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.847393 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): 31.96600 81.47400 ymin,ymax (A): 25.28900 81.55100 zmin,zma (A): -2.859000 46.34600 x,y,z range (A): 49.50800 56.26200 49.20500 scale (grids/A): 2.847393 object centre (A): 56.72000 53.42000 21.74350 number of atom coordinates read : 3338 total number of charged atoms : 3187 net assigned charge : -6.999975 assigned positive charge : 508.5882 centred at (gu) : 93.98477 88.30328 94.78141 assigned negative charge : -515.5894 centred at (gu) : 93.00340 88.73241 94.51940 start vw surface at 0.1300000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 219416 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24533 grid for indexing accessible points = 1.400000 m= 117810 mr = 168073 m= 46156 mr = 100505 m= 11674 mr = 39297 m= 1611 mr = 9372 m= 69 mr = 1168 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 8686 time to turn everything in is 1.550000 number of dielectric boundary points 78298 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 25496 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) : 1.898262 object centre at (A) : 56.72000 53.42000 21.74350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2702815 -0.2586775 midg,1,midg; midg,igrid,midg -1.1146631E-02 -4.6546650E-03 1,midg,midg; igrid,midg,midg -0.4408480 0.2287730 gauss-seidel spectral radius is 0.9992725 estimated iterations to convergence 293 setup time was (sec) 1.780000 now iterating at: 11:31:49 rms-change max change #iterations 11.42179 333.3446 at 10iterations 6.704004 147.2258 at 20iterations 3.895587 66.91211 at 30iterations 2.262396 41.03742 at 40iterations 1.314965 25.32433 at 50iterations 0.7616013 13.31149 at 60iterations 0.4415689 7.340261 at 70iterations 0.2555068 4.240076 at 80iterations 0.1477827 2.311153 at 90iterations 8.5317083E-02 1.382317 at 100iterations 4.9374208E-02 0.8010502 at 110iterations 2.8554987E-02 0.4367638 at 120iterations 1.6530721E-02 0.2701874 at 130iterations 9.5458822E-03 0.1492524 at 140iterations 5.5240900E-03 8.9321136E-02 at 150iterations 3.1975708E-03 5.2627563E-02 at 160iterations 1.8489660E-03 3.3645630E-02 at 170iterations 1.0684138E-03 1.7578125E-02 at 180iterations finished qdiffx linear iterations at : 11:32:01 total time elapsed so far: 13.45000 # loops : 180 mean,max change (kT/e) : 1.0684138E-03 1.7578125E-02 energy calculations done at 13.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.60000 DelPhi exited at 11:32:01 13.601u 0.232s 0:14.19 97.4% 0+0k 0+45360io 0pf+0w