Sat Oct 8 17:33:04 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 17:33:04 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3547 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5244550 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): -1.320000 44.56100 ymin,ymax (A): -30.42900 25.94400 zmin,zma (A): 1.593000 69.47300 x,y,z range (A): 45.88100 56.37300 67.88000 scale (grids/A): 0.5244550 object centre (A): 21.62050 -2.242499 35.53300 number of atom coordinates read : 3547 total number of charged atoms : 3400 net assigned charge : -5.871980 assigned positive charge : 544.4720 centred at (gu) : 90.39718 91.65465 90.51282 assigned negative charge : -550.3459 centred at (gu) : 90.36141 91.61446 90.50282 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6156 nv = 96 ne = 84 npr = 72745 no. pairs analyzed = 72745 no. exposed pairs = 4313 no. arc points = 29721 no. surface atoms = 1465 nbur = 2082 mkacc time = 0.1500000 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 = 1.624000 m= 217 mr = 3260 m= 0 mr = 11 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3102 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2943 ## 411 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8191 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6757257E-10 -1.3579914E-10 midg,1,midg; midg,igrid,midg -1.9641247E-10 -1.5933185E-11 1,midg,midg; igrid,midg,midg -2.5539287E-10 -3.1173876E-11 gauss-seidel spectral radius is 0.9813071 estimated iterations to convergence 60 setup time was (sec) 0.5800000 now iterating at: 17:33:05 rms-change max change #iterations 6.7600809E-02 10.74557 at 10iterations 4.3353671E-03 0.7127142 at 20iterations 4.3996095E-04 7.6568604E-02 at 30iterations 1.0468169E-04 2.0215988E-02 at 40iterations 2.9383193E-05 5.4588318E-03 at 50iterations finished qdiffx linear iterations at : 17:33:08 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 2.9383193E-05 5.4588318E-03 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 17:33:09 3.686u 0.215s 0:04.16 93.5% 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 17:33:09 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3547 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.573365 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): -1.320000 44.56100 ymin,ymax (A): -30.42900 25.94400 zmin,zma (A): 1.593000 69.47300 x,y,z range (A): 45.88100 56.37300 67.88000 scale (grids/A): 1.573365 object centre (A): 21.62050 -2.242499 35.53300 number of atom coordinates read : 3547 total number of charged atoms : 3400 net assigned charge : -5.871980 assigned positive charge : 544.4720 centred at (gu) : 91.19040 94.96304 91.53762 assigned negative charge : -550.3459 centred at (gu) : 91.08403 94.84298 91.50810 start vw surface at 0.1800000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 69154 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29721 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20739 mr = 47948 m= 1950 mr = 14250 m= 50 mr = 880 m= 0 mr = 4 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 28811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 425 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 25759 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) : 0.5244550 object centre at (A) : 21.62050 -2.242499 35.53300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9619636E-03 1.3022727E-02 midg,1,midg; midg,igrid,midg -8.2836216E-03 -1.0615023E-02 1,midg,midg; igrid,midg,midg -3.9425562E-03 5.6365115E-04 gauss-seidel spectral radius is 0.9980822 estimated iterations to convergence 181 setup time was (sec) 0.8400000 now iterating at: 17:33:10 rms-change max change #iterations 3.427798 149.7359 at 10iterations 1.391442 52.78773 at 20iterations 0.5657436 20.03192 at 30iterations 0.2316534 8.009911 at 40iterations 9.4376728E-02 3.731068 at 50iterations 3.8459141E-02 1.460058 at 60iterations 1.5658336E-02 0.5898342 at 70iterations 6.4406623E-03 0.2212391 at 80iterations 2.6514991E-03 9.8098755E-02 at 90iterations 1.1139200E-03 4.0262222E-02 at 100iterations 4.8625690E-04 1.7568588E-02 at 110iterations 2.2707951E-04 8.4609985E-03 at 120iterations finished qdiffx linear iterations at : 17:33:17 total time elapsed so far: 8.430000 # loops : 120 mean,max change (kT/e) : 2.2707951E-04 8.4609985E-03 energy calculations done at 8.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.600000 DelPhi exited at 17:33:18 8.600u 0.257s 0:09.16 96.6% 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 Sat Oct 8 2011 at 17:33:18 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3547 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.360047 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): -1.320000 44.56100 ymin,ymax (A): -30.42900 25.94400 zmin,zma (A): 1.593000 69.47300 x,y,z range (A): 45.88100 56.37300 67.88000 scale (grids/A): 2.360047 object centre (A): 21.62050 -2.242499 35.53300 number of atom coordinates read : 3547 total number of charged atoms : 3400 net assigned charge : -5.871980 assigned positive charge : 544.4720 centred at (gu) : 91.78554 97.44424 92.30591 assigned negative charge : -550.3459 centred at (gu) : 91.62592 97.26431 92.26218 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 160667 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29721 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 73910 mr = 117295 m= 19711 mr = 58483 m= 2788 mr = 14560 m= 158 mr = 1734 m= 2 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.200000 number of dielectric boundary points 65101 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 27142 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) : 1.573365 object centre at (A) : 21.62050 -2.242499 35.53300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2886941 0.1622705 midg,1,midg; midg,igrid,midg -0.1137948 -0.1503693 1,midg,midg; igrid,midg,midg -6.5806970E-02 3.7325732E-02 gauss-seidel spectral radius is 0.9991114 estimated iterations to convergence 265 setup time was (sec) 1.530000 now iterating at: 17:33:20 rms-change max change #iterations 9.047698 243.3281 at 10iterations 5.010586 109.7076 at 20iterations 2.771838 66.91978 at 30iterations 1.521554 32.83997 at 40iterations 0.8345630 17.45127 at 50iterations 0.4548655 9.851595 at 60iterations 0.2490324 5.042225 at 70iterations 0.1359998 2.691496 at 80iterations 7.4217960E-02 1.683730 at 90iterations 4.0499602E-02 0.8176956 at 100iterations 2.2071272E-02 0.4690552 at 110iterations 1.2026920E-02 0.2465878 at 120iterations 6.5642027E-03 0.1320658 at 130iterations 3.5753085E-03 7.0679545E-02 at 140iterations 1.9597595E-03 4.1290283E-02 at 150iterations 1.0774386E-03 2.1749496E-02 at 160iterations 5.9905747E-04 1.2588024E-02 at 170iterations 3.3746019E-04 7.5569153E-03 at 180iterations finished qdiffx linear iterations at : 17:33:34 total time elapsed so far: 16.38000 # loops : 180 mean,max change (kT/e) : 3.3746019E-04 7.5569153E-03 energy calculations done at 16.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.55000 DelPhi exited at 17:33:35 16.547u 0.270s 0:17.09 98.3% 0+0k 0+0io 0pf+0w