Mon Oct 10 14:16:10 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+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 Mon Oct 10 2011 at 14:16:10 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3959 !!! WARNING: ADP 663 has a net charge of -2.0000 !!! WARNING: MG6 664 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5198598 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): -1.982000 51.52900 ymin,ymax (A): -16.03000 47.84500 zmin,zma (A): -21.28100 47.19900 x,y,z range (A): 53.51100 63.87500 68.48000 scale (grids/A): 0.5198598 object centre (A): 24.77350 15.90750 12.95900 number of atom coordinates read : 3959 total number of charged atoms : 3775 net assigned charge : -8.099981 assigned positive charge : 617.9865 centred at (gu) : 89.32854 89.64871 89.97734 assigned negative charge : -626.0896 centred at (gu) : 89.39577 89.66909 90.06242 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7088 nv = 96 ne = 84 npr = 74170 no. pairs analyzed = 74170 no. exposed pairs = 6047 no. arc points = 41576 no. surface atoms = 1981 nbur = 1978 mkacc time = 0.2100000 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= 309 mr = 3155 m= 1 mr = 5 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 0.4600000 number of dielectric boundary points 4238 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4022 ## 534 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 9250 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0865752E-10 -4.6052648E-10 midg,1,midg; midg,igrid,midg -1.1576085E-10 -2.2224320E-10 1,midg,midg; igrid,midg,midg 6.0384961E-11 -3.3827535E-10 gauss-seidel spectral radius is 0.9810338 estimated iterations to convergence 60 setup time was (sec) 0.7300000 now iterating at: 14:16:11 rms-change max change #iterations 6.9366395E-02 10.38290 at 10iterations 4.6105455E-03 0.7381897 at 20iterations 8.0244313E-04 0.1015491 at 30iterations 2.7448183E-04 3.6087036E-02 at 40iterations 1.0132143E-04 1.3084412E-02 at 50iterations finished qdiffx linear iterations at : 14:16:14 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 1.0132143E-04 1.3084412E-02 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 14:16:15 4.210u 0.245s 0:04.79 92.9% 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 Mon Oct 10 2011 at 14:16:15 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3959 !!! WARNING: ADP 663 has a net charge of -2.0000 !!! WARNING: MG6 664 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.559579 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): -1.982000 51.52900 ymin,ymax (A): -16.03000 47.84500 zmin,zma (A): -21.28100 47.19900 x,y,z range (A): 53.51100 63.87500 68.48000 scale (grids/A): 1.559579 object centre (A): 24.77350 15.90750 12.95900 number of atom coordinates read : 3959 total number of charged atoms : 3775 net assigned charge : -8.099981 assigned positive charge : 617.9865 centred at (gu) : 87.98421 88.94463 89.93051 assigned negative charge : -626.0896 centred at (gu) : 88.18711 89.00690 90.18697 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 79084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41576 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 22520 mr = 50154 m= 2095 mr = 13425 m= 42 mr = 759 m= 0 mr = 1 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 39402 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 478 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 28534 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) : 0.5198598 object centre at (A) : 24.77350 15.90750 12.95900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1602764E-02 -1.6631581E-02 midg,1,midg; midg,igrid,midg 7.2443002E-04 8.3272336E-03 1,midg,midg; igrid,midg,midg -3.4372627E-03 -1.6680708E-02 gauss-seidel spectral radius is 0.9981393 estimated iterations to convergence 184 setup time was (sec) 1.010000 now iterating at: 14:16:16 rms-change max change #iterations 3.668693 144.3018 at 10iterations 1.491976 57.64519 at 20iterations 0.6130499 22.47067 at 30iterations 0.2514316 9.889168 at 40iterations 0.1037840 3.604737 at 50iterations 4.2618051E-02 1.528709 at 60iterations 1.7595230E-02 0.6184702 at 70iterations 7.3428894E-03 0.2472229 at 80iterations 3.1387808E-03 0.1110382 at 90iterations 1.3993984E-03 5.0889969E-02 at 100iterations 6.8960618E-04 2.2960663E-02 at 110iterations 3.8198021E-04 1.2837410E-02 at 120iterations finished qdiffx linear iterations at : 14:16:25 total time elapsed so far: 9.430000 # loops : 120 mean,max change (kT/e) : 3.8198021E-04 1.2837410E-02 energy calculations done at 9.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.610000 DelPhi exited at 14:16:25 9.612u 0.312s 0:10.47 94.7% 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 Mon Oct 10 2011 at 14:16:25 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3959 !!! WARNING: ADP 663 has a net charge of -2.0000 !!! WARNING: MG6 664 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.339369 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): -1.982000 51.52900 ymin,ymax (A): -16.03000 47.84500 zmin,zma (A): -21.28100 47.19900 x,y,z range (A): 53.51100 63.87500 68.48000 scale (grids/A): 2.339369 object centre (A): 24.77350 15.90750 12.95900 number of atom coordinates read : 3959 total number of charged atoms : 3775 net assigned charge : -8.099981 assigned positive charge : 617.9865 centred at (gu) : 86.97599 88.41694 89.89552 assigned negative charge : -626.0896 centred at (gu) : 87.28045 88.51022 90.28038 start vw surface at 0.2000000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 183932 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41576 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 79837 mr = 125028 m= 20441 mr = 58155 m= 2911 mr = 13380 m= 181 mr = 1561 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.760000 number of dielectric boundary points 89132 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 30132 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) : 1.559579 object centre at (A) : 24.77350 15.90750 12.95900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2335541 -0.3453749 midg,1,midg; midg,igrid,midg 9.9953795E-03 0.1804641 1,midg,midg; igrid,midg,midg -2.7435131E-02 -0.2581410 gauss-seidel spectral radius is 0.9991724 estimated iterations to convergence 275 setup time was (sec) 2.100000 now iterating at: 14:16:28 rms-change max change #iterations 10.14574 319.9433 at 10iterations 5.970592 169.4023 at 20iterations 3.475110 95.45753 at 30iterations 2.002643 50.00738 at 40iterations 1.144012 26.50035 at 50iterations 0.6519051 19.15745 at 60iterations 0.3695974 8.388260 at 70iterations 0.2089985 4.873886 at 80iterations 0.1178144 2.834615 at 90iterations 6.6303983E-02 1.652153 at 100iterations 3.7327766E-02 0.8496418 at 110iterations 2.0922661E-02 0.4386063 at 120iterations 1.1752294E-02 0.2487187 at 130iterations 6.5894248E-03 0.1381893 at 140iterations 3.6860304E-03 8.7491989E-02 at 150iterations 2.0635740E-03 3.9926529E-02 at 160iterations 1.1594273E-03 2.3017883E-02 at 170iterations 6.5263128E-04 1.3450623E-02 at 180iterations finished qdiffx linear iterations at : 14:16:42 total time elapsed so far: 16.43000 # loops : 180 mean,max change (kT/e) : 6.5263128E-04 1.3450623E-02 energy calculations done at 16.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.61000 DelPhi exited at 14:16:43 16.610u 0.293s 0:17.39 97.1% 0+0k 0+0io 0pf+0w