Sat Oct 15 14:31:05 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 15 2011 at 14:31:05 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2904 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: ASP 354 has a net charge of -0.5000 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: 0.6059059 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): -27.24500 31.51000 ymin,ymax (A): -10.28800 39.52400 zmin,zma (A): 6.416000 61.40600 x,y,z range (A): 58.75500 49.81200 54.99000 scale (grids/A): 0.6059059 object centre (A): 2.132501 14.61800 33.91100 number of atom coordinates read : 2904 total number of charged atoms : 2763 net assigned charge : -4.485967 assigned positive charge : 441.8470 centred at (gu) : 91.31273 90.42931 91.02956 assigned negative charge : -446.3342 centred at (gu) : 91.40923 90.30611 91.13335 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7068 nv = 96 ne = 84 npr = 58346 no. pairs analyzed = 58346 no. exposed pairs = 3775 no. arc points = 26740 no. surface atoms = 1265 nbur = 1639 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 333 mr = 3657 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.3500000 number of dielectric boundary points 3725 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2709 ## 277 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8876 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2993294E-09 -9.4412203E-09 midg,1,midg; midg,igrid,midg -7.6891391E-09 4.2974948E-09 1,midg,midg; igrid,midg,midg 1.8860404E-09 -9.5667607E-09 gauss-seidel spectral radius is 0.9859288 estimated iterations to convergence 69 setup time was (sec) 0.7100000 now iterating at: 14:31:07 rms-change max change #iterations 0.1232617 20.81488 at 10iterations 1.0636386E-02 1.377650 at 20iterations 9.3014323E-04 0.1240873 at 30iterations 8.2695246E-05 1.4457703E-02 at 40iterations 7.3914262E-06 1.0890961E-03 at 50iterations finished qdiffx linear iterations at : 14:31:14 total time elapsed so far: 5.170000 # loops : 50 mean,max change (kT/e) : 7.3914262E-06 1.0890961E-03 energy calculations done at 5.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.330000 DelPhi exited at 14:31:16 5.337u 0.496s 0:10.37 56.1% 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 Sat Oct 15 2011 at 14:31:16 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2904 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: ASP 354 has a net charge of -0.5000 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: 1.817718 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): -27.24500 31.51000 ymin,ymax (A): -10.28800 39.52400 zmin,zma (A): 6.416000 61.40600 x,y,z range (A): 58.75500 49.81200 54.99000 scale (grids/A): 1.817718 object centre (A): 2.132501 14.61800 33.91100 number of atom coordinates read : 2904 total number of charged atoms : 2763 net assigned charge : -4.485967 assigned positive charge : 441.8470 centred at (gu) : 93.93742 91.28677 93.08790 assigned negative charge : -446.3342 centred at (gu) : 94.22699 90.91783 93.39953 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 77229 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26740 grid for indexing accessible points = 1.400000 m= 25497 mr = 52397 m= 3307 mr = 17761 m= 160 mr = 1756 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 841 time to turn everything in is 0.6500000 number of dielectric boundary points 34253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 222 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 21635 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) : 0.6059059 object centre at (A) : 2.132501 14.61800 33.91100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.7115068E-03 -5.2983272E-03 midg,1,midg; midg,igrid,midg -2.0895114E-02 4.5670527E-03 1,midg,midg; igrid,midg,midg 2.6453141E-02 -5.5594046E-02 gauss-seidel spectral radius is 0.9985383 estimated iterations to convergence 207 setup time was (sec) 1.000000 now iterating at: 14:31:21 rms-change max change #iterations 4.202873 180.7983 at 10iterations 1.900362 67.12200 at 20iterations 0.8667763 28.70387 at 30iterations 0.3947617 12.79315 at 40iterations 0.1791063 5.963352 at 50iterations 8.1720069E-02 2.587827 at 60iterations 3.7179120E-02 1.216335 at 70iterations 1.6972383E-02 0.6222572 at 80iterations 7.7394387E-03 0.2322540 at 90iterations 3.5210093E-03 0.1070776 at 100iterations 1.6129342E-03 5.5130005E-02 at 110iterations 7.3454558E-04 2.4964333E-02 at 120iterations finished qdiffx linear iterations at : 14:31:43 total time elapsed so far: 12.24000 # loops : 120 mean,max change (kT/e) : 7.3454558E-04 2.4964333E-02 energy calculations done at 12.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.40000 DelPhi exited at 14:31:45 12.407u 0.546s 0:28.68 45.1% 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 Sat Oct 15 2011 at 14:31:45 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2904 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: ASP 354 has a net charge of -0.5000 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: 2.726577 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): -27.24500 31.51000 ymin,ymax (A): -10.28800 39.52400 zmin,zma (A): 6.416000 61.40600 x,y,z range (A): 58.75500 49.81200 54.99000 scale (grids/A): 2.726577 object centre (A): 2.132501 14.61800 33.91100 number of atom coordinates read : 2904 total number of charged atoms : 2763 net assigned charge : -4.485967 assigned positive charge : 441.8470 centred at (gu) : 95.90580 91.93002 94.63161 assigned negative charge : -446.3342 centred at (gu) : 96.34034 91.37670 95.09933 start vw surface at 0.1200000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 178916 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26740 grid for indexing accessible points = 1.400000 m= 85466 mr = 127793 m= 27375 mr = 67876 m= 5353 mr = 20875 m= 622 mr = 3543 m= 21 mr = 359 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 2835 time to turn everything in is 1.670000 number of dielectric boundary points 77302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 22099 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) : 1.817718 object centre at (A) : 2.132501 14.61800 33.91100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5719214E-03 0.1300950 midg,1,midg; midg,igrid,midg -0.2236438 7.2205976E-02 1,midg,midg; igrid,midg,midg 0.3761412 -0.6214615 gauss-seidel spectral radius is 0.9992484 estimated iterations to convergence 288 setup time was (sec) 2.060000 now iterating at: 14:31:50 rms-change max change #iterations 10.28456 336.5335 at 10iterations 6.051024 165.4889 at 20iterations 3.534742 80.58736 at 30iterations 2.051162 52.87275 at 40iterations 1.184273 26.14851 at 50iterations 0.6843334 12.15145 at 60iterations 0.3931763 7.997426 at 70iterations 0.2264354 4.629117 at 80iterations 0.1301918 2.319366 at 90iterations 7.4644715E-02 1.455730 at 100iterations 4.2785190E-02 0.7571602 at 110iterations 2.4574185E-02 0.4817514 at 120iterations 1.4037859E-02 0.2686691 at 130iterations 8.0421008E-03 0.1476173 at 140iterations 4.6074698E-03 8.9120865E-02 at 150iterations 2.6361183E-03 5.8082581E-02 at 160iterations 1.5078782E-03 3.1095028E-02 at 170iterations 8.6495548E-04 1.6799927E-02 at 180iterations finished qdiffx linear iterations at : 14:32:34 total time elapsed so far: 22.14000 # loops : 180 mean,max change (kT/e) : 8.6495548E-04 1.6799927E-02 energy calculations done at 22.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.31000 DelPhi exited at 14:32:35 22.310u 0.647s 0:49.80 46.0% 0+0k 0+0io 0pf+0w