Sun Oct 9 04:41:27 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 Sun Oct 9 2011 at 04:41:27 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2693 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5894527 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): 29.69700 75.83200 ymin,ymax (A): 10.05000 70.44500 zmin,zma (A): -27.76200 24.54200 x,y,z range (A): 46.13500 60.39500 52.30400 scale (grids/A): 0.5894527 object centre (A): 52.76450 40.24750 -1.610000 number of atom coordinates read : 2693 total number of charged atoms : 2554 net assigned charge : 5.500028 assigned positive charge : 402.7162 centred at (gu) : 90.03272 91.50259 89.93980 assigned negative charge : -397.2173 centred at (gu) : 90.10264 91.50027 89.92795 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6170 nv = 96 ne = 84 npr = 53965 no. pairs analyzed = 53965 no. exposed pairs = 3676 no. arc points = 25537 no. surface atoms = 1228 nbur = 1465 mkacc time = 0.1200000 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 = 1.456000 m= 325 mr = 3059 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3422 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2505 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7723 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3588575E-09 1.9476769E-09 midg,1,midg; midg,igrid,midg 1.1454713E-09 2.4140328E-09 1,midg,midg; igrid,midg,midg 3.4849277E-09 -2.2823889E-10 gauss-seidel spectral radius is 0.9851213 estimated iterations to convergence 67 setup time was (sec) 0.5800000 now iterating at: 04:41:28 rms-change max change #iterations 0.1030374 20.10135 at 10iterations 8.1859231E-03 1.472856 at 20iterations 6.9267332E-04 0.1008015 at 30iterations 9.1325492E-05 1.6423225E-02 at 40iterations 2.9427136E-05 5.0659180E-03 at 50iterations finished qdiffx linear iterations at : 04:41:32 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 2.9427136E-05 5.0659180E-03 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 04:41:32 4.274u 0.267s 0:04.81 94.1% 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 Sun Oct 9 2011 at 04:41:32 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2693 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.768358 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): 29.69700 75.83200 ymin,ymax (A): 10.05000 70.44500 zmin,zma (A): -27.76200 24.54200 x,y,z range (A): 46.13500 60.39500 52.30400 scale (grids/A): 1.768358 object centre (A): 52.76450 40.24750 -1.610000 number of atom coordinates read : 2693 total number of charged atoms : 2554 net assigned charge : 5.500028 assigned positive charge : 402.7162 centred at (gu) : 90.09749 94.50709 89.81898 assigned negative charge : -397.2173 centred at (gu) : 90.30760 94.50065 89.78336 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 67205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25537 grid for indexing accessible points = 1.400000 m= 21402 mr = 44573 m= 2773 mr = 14333 m= 122 mr = 1371 m= 2 mr = 24 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 0.5100000 number of dielectric boundary points 31203 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 199 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 19847 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) : 0.5894527 object centre at (A) : 52.76450 40.24750 -1.610000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2161259E-03 1.0535470E-02 midg,1,midg; midg,igrid,midg -1.9047474E-02 2.0193893E-02 1,midg,midg; igrid,midg,midg 1.4691543E-02 2.9677714E-03 gauss-seidel spectral radius is 0.9984362 estimated iterations to convergence 201 setup time was (sec) 0.8600000 now iterating at: 04:41:33 rms-change max change #iterations 3.736250 159.3125 at 10iterations 1.648430 59.20177 at 20iterations 0.7293621 31.72509 at 30iterations 0.3253162 11.36272 at 40iterations 0.1439143 4.965649 at 50iterations 6.3900642E-02 2.210128 at 60iterations 2.8282303E-02 1.030830 at 70iterations 1.2604706E-02 0.4143639 at 80iterations 5.6149531E-03 0.1882629 at 90iterations 2.4877053E-03 8.4829330E-02 at 100iterations 1.1163981E-03 3.5837889E-02 at 110iterations 5.0130708E-04 1.7473221E-02 at 120iterations finished qdiffx linear iterations at : 04:41:42 total time elapsed so far: 9.800000 # loops : 120 mean,max change (kT/e) : 5.0130708E-04 1.7473221E-02 energy calculations done at 9.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.970000 DelPhi exited at 04:41:43 9.973u 0.331s 0:10.60 97.1% 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 Sun Oct 9 2011 at 04:41:43 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2693 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.652537 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): 29.69700 75.83200 ymin,ymax (A): 10.05000 70.44500 zmin,zma (A): -27.76200 24.54200 x,y,z range (A): 46.13500 60.39500 52.30400 scale (grids/A): 2.652537 object centre (A): 52.76450 40.24750 -1.610000 number of atom coordinates read : 2693 total number of charged atoms : 2554 net assigned charge : 5.500028 assigned positive charge : 402.7162 centred at (gu) : 90.14588 96.76048 89.72821 assigned negative charge : -397.2173 centred at (gu) : 90.46143 96.75088 89.67500 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 155887 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25537 grid for indexing accessible points = 1.400000 m= 72173 mr = 109434 m= 22511 mr = 55965 m= 4518 mr = 16622 m= 497 mr = 2898 m= 22 mr = 248 m= 0 mr = 8 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.320000 number of dielectric boundary points 70433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 20416 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) : 1.768358 object centre at (A) : 52.76450 40.24750 -1.610000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5516071E-02 0.1467686 midg,1,midg; midg,igrid,midg -0.2541063 0.2986738 1,midg,midg; igrid,midg,midg 0.1547557 4.2077038E-02 gauss-seidel spectral radius is 0.9992110 estimated iterations to convergence 281 setup time was (sec) 1.680000 now iterating at: 04:41:45 rms-change max change #iterations 9.307648 331.5378 at 10iterations 5.421396 146.3940 at 20iterations 3.118920 83.55656 at 30iterations 1.788533 37.62983 at 40iterations 1.023181 26.14210 at 50iterations 0.5828533 15.32275 at 60iterations 0.3319328 8.607840 at 70iterations 0.1885115 3.823174 at 80iterations 0.1070634 2.270049 at 90iterations 6.0580239E-02 1.222727 at 100iterations 3.4293715E-02 0.7279549 at 110iterations 1.9395698E-02 0.3914614 at 120iterations 1.0969377E-02 0.2469044 at 130iterations 6.2240828E-03 0.1485023 at 140iterations 3.5357005E-03 8.3827019E-02 at 150iterations 2.0145986E-03 4.4672012E-02 at 160iterations 1.1617489E-03 2.5321960E-02 at 170iterations 6.8530015E-04 1.5522003E-02 at 180iterations finished qdiffx linear iterations at : 04:41:59 total time elapsed so far: 15.74000 # loops : 180 mean,max change (kT/e) : 6.8530015E-04 1.5522003E-02 energy calculations done at 15.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.92000 DelPhi exited at 04:41:59 15.924u 0.329s 0:16.51 98.3% 0+0k 0+0io 0pf+0w