Sat Oct 8 14:13:23 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 14:13:23 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2947 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 0.6309596 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): -11.35000 43.28300 ymin,ymax (A): 10.51400 55.06800 zmin,zma (A): 36.04800 92.47000 x,y,z range (A): 54.63300 44.55400 56.42200 scale (grids/A): 0.6309596 object centre (A): 15.96650 32.79100 64.25900 number of atom coordinates read : 2947 total number of charged atoms : 2801 net assigned charge : 1.4008060E-02 assigned positive charge : 441.6377 centred at (gu) : 89.32734 89.55958 92.07398 assigned negative charge : -441.6245 centred at (gu) : 89.30825 89.46638 92.02974 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7923 nv = 96 ne = 84 npr = 60998 no. pairs analyzed = 60998 no. exposed pairs = 3357 no. arc points = 23295 no. surface atoms = 1151 nbur = 1796 mkacc time = 0.2000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 405 mr = 4708 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3580 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2252 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9560 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9219469E-09 7.1682629E-09 midg,1,midg; midg,igrid,midg -1.0703306E-08 8.5890797E-09 1,midg,midg; igrid,midg,midg -2.3107227E-09 1.6700448E-09 gauss-seidel spectral radius is 0.9870144 estimated iterations to convergence 72 setup time was (sec) 0.7000000 now iterating at: 14:13:24 rms-change max change #iterations 0.1530095 22.93759 at 10iterations 1.5236489E-02 2.065893 at 20iterations 1.5945514E-03 0.2382565 at 30iterations 2.1505851E-04 2.8713226E-02 at 40iterations 4.0268249E-05 6.5164566E-03 at 50iterations finished qdiffx linear iterations at : 14:13:29 total time elapsed so far: 5.160000 # loops : 50 mean,max change (kT/e) : 4.0268249E-05 6.5164566E-03 energy calculations done at 5.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.340000 DelPhi exited at 14:13:29 5.349u 0.462s 0:06.09 95.2% 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 14:13:29 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2947 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 1.892879 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): -11.35000 43.28300 ymin,ymax (A): 10.51400 55.06800 zmin,zma (A): 36.04800 92.47000 x,y,z range (A): 54.63300 44.55400 56.42200 scale (grids/A): 1.892879 object centre (A): 15.96650 32.79100 64.25900 number of atom coordinates read : 2947 total number of charged atoms : 2801 net assigned charge : 1.4008060E-02 assigned positive charge : 441.6377 centred at (gu) : 87.98177 88.67804 96.22144 assigned negative charge : -441.6245 centred at (gu) : 87.92468 88.39871 96.08899 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 86870 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23295 grid for indexing accessible points = 1.400000 m= 32277 mr = 63411 m= 4710 mr = 24570 m= 240 mr = 2878 m= 6 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 132 time to turn everything in is 0.7100000 number of dielectric boundary points 33184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 22026 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) : 0.6309596 object centre at (A) : 15.96650 32.79100 64.25900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5135204E-02 3.0431818E-04 midg,1,midg; midg,igrid,midg -3.6462916E-03 1.2401403E-02 1,midg,midg; igrid,midg,midg 5.7936101E-03 1.9434275E-02 gauss-seidel spectral radius is 0.9986469 estimated iterations to convergence 215 setup time was (sec) 1.060000 now iterating at: 14:13:31 rms-change max change #iterations 4.560517 169.4246 at 10iterations 2.147737 69.35820 at 20iterations 1.011318 30.03266 at 30iterations 0.4763642 16.55897 at 40iterations 0.2243648 6.771484 at 50iterations 0.1053195 3.213085 at 60iterations 4.9588289E-02 1.540625 at 70iterations 2.3336614E-02 0.6651306 at 80iterations 1.1067522E-02 0.3312716 at 90iterations 5.2018664E-03 0.1686945 at 100iterations 2.4628006E-03 7.8687668E-02 at 110iterations 1.1673993E-03 3.3298492E-02 at 120iterations finished qdiffx linear iterations at : 14:13:42 total time elapsed so far: 12.58000 # loops : 120 mean,max change (kT/e) : 1.1673993E-03 3.3298492E-02 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 14:13:43 12.758u 0.529s 0:13.61 97.5% 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 14:13:43 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2947 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 2.839318 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): -11.35000 43.28300 ymin,ymax (A): 10.51400 55.06800 zmin,zma (A): 36.04800 92.47000 x,y,z range (A): 54.63300 44.55400 56.42200 scale (grids/A): 2.839318 object centre (A): 15.96650 32.79100 64.25900 number of atom coordinates read : 2947 total number of charged atoms : 2801 net assigned charge : 1.4008060E-02 assigned positive charge : 441.6377 centred at (gu) : 86.97243 88.01695 99.33185 assigned negative charge : -441.6245 centred at (gu) : 86.88706 87.59804 99.13338 start vw surface at 0.1200000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 201378 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23295 grid for indexing accessible points = 1.400000 m= 105587 mr = 152986 m= 37593 mr = 88859 m= 8274 mr = 30539 m= 1066 mr = 6044 m= 51 mr = 701 m= 0 mr = 9 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 479 time to turn everything in is 1.890000 number of dielectric boundary points 74811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.090000 number of grid points assigned charge 22403 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) : 1.892879 object centre at (A) : 15.96650 32.79100 64.25900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1090917E-02 8.8931575E-02 midg,1,midg; midg,igrid,midg -2.9735342E-02 0.1433151 1,midg,midg; igrid,midg,midg 0.2340034 0.3584011 gauss-seidel spectral radius is 0.9992654 estimated iterations to convergence 291 setup time was (sec) 2.320000 now iterating at: 14:13:46 rms-change max change #iterations 10.68236 338.9940 at 10iterations 6.272346 135.0082 at 20iterations 3.651659 71.41257 at 30iterations 2.130741 44.45401 at 40iterations 1.237663 23.56236 at 50iterations 0.7163075 12.60772 at 60iterations 0.4151673 7.776600 at 70iterations 0.2396334 4.342577 at 80iterations 0.1385238 2.345749 at 90iterations 8.0078587E-02 1.418876 at 100iterations 4.6277981E-02 0.7236671 at 110iterations 2.6707232E-02 0.4432650 at 120iterations 1.5387875E-02 0.2601166 at 130iterations 8.8948887E-03 0.1557236 at 140iterations 5.1466879E-03 8.3721161E-02 at 150iterations 2.9800613E-03 4.7461987E-02 at 160iterations 1.7338353E-03 2.9052734E-02 at 170iterations 1.0157761E-03 1.7013311E-02 at 180iterations finished qdiffx linear iterations at : 14:14:05 total time elapsed so far: 21.78000 # loops : 180 mean,max change (kT/e) : 1.0157761E-03 1.7013311E-02 energy calculations done at 21.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.95000 DelPhi exited at 14:14:06 21.956u 0.552s 0:22.79 98.7% 0+0k 0+0io 0pf+0w