Mon Oct 10 17:04:58 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 Mon Oct 10 2011 at 17:04:58 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5120 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5047498 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): -14.27100 47.62800 ymin,ymax (A): -28.06900 34.21300 zmin,zma (A): 15.59600 86.12600 x,y,z range (A): 61.89900 62.28200 70.53000 scale (grids/A): 0.5047498 object centre (A): 16.67850 3.072001 50.86100 number of atom coordinates read : 5120 total number of charged atoms : 4858 net assigned charge : 8.300034 assigned positive charge : 769.9830 centred at (gu) : 89.16793 90.06237 89.80985 assigned negative charge : -761.6888 centred at (gu) : 89.21461 90.02735 89.77608 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8137 nv = 96 ne = 84 npr = 103845 no. pairs analyzed = 103845 no. exposed pairs = 6371 no. arc points = 43580 no. surface atoms = 2157 nbur = 2963 mkacc time = 0.2200000 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 = 1.680000 m= 269 mr = 4214 m= 2 mr = 1 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 0.4700000 number of dielectric boundary points 4193 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4295 ## 687 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 10948 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7376846E-11 1.5393933E-10 midg,1,midg; midg,igrid,midg 1.3837493E-11 1.6723838E-10 1,midg,midg; igrid,midg,midg 2.3621463E-10 -8.3394012E-12 gauss-seidel spectral radius is 0.9799498 estimated iterations to convergence 58 setup time was (sec) 0.6900000 now iterating at: 17:04:59 rms-change max change #iterations 6.6704176E-02 10.62614 at 10iterations 5.6039449E-03 1.212929 at 20iterations 1.7512493E-03 0.4013290 at 30iterations 7.0743979E-04 0.1547127 at 40iterations 2.9133703E-04 6.0661316E-02 at 50iterations finished qdiffx linear iterations at : 17:05:01 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 2.9133703E-04 6.0661316E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 17:05:03 3.435u 0.193s 0:04.91 73.7% 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 17:05:03 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5120 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.514249 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): -14.27100 47.62800 ymin,ymax (A): -28.06900 34.21300 zmin,zma (A): 15.59600 86.12600 x,y,z range (A): 61.89900 62.28200 70.53000 scale (grids/A): 1.514249 object centre (A): 16.67850 3.072001 50.86100 number of atom coordinates read : 5120 total number of charged atoms : 4858 net assigned charge : 8.300034 assigned positive charge : 769.9830 centred at (gu) : 87.50234 90.18545 89.42791 assigned negative charge : -761.6888 centred at (gu) : 87.64376 90.08174 89.32793 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 93076 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43580 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26034 mr = 64486 m= 2197 mr = 16846 m= 47 mr = 820 m= 0 mr = 2 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 39200 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 643 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 36495 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) : 0.5047498 object centre at (A) : 16.67850 3.072001 50.86100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8569930E-02 9.0257935E-03 midg,1,midg; midg,igrid,midg 1.7698631E-03 2.5234716E-03 1,midg,midg; igrid,midg,midg 1.4413647E-02 -2.4272648E-03 gauss-seidel spectral radius is 0.9980899 estimated iterations to convergence 182 setup time was (sec) 0.9600000 now iterating at: 17:05:04 rms-change max change #iterations 3.850587 183.2228 at 10iterations 1.564067 55.39689 at 20iterations 0.6389921 21.48366 at 30iterations 0.2607217 8.399632 at 40iterations 0.1065446 3.575653 at 50iterations 4.3744877E-02 1.402170 at 60iterations 1.8380815E-02 0.5630009 at 70iterations 8.0617648E-03 0.2838593 at 80iterations 3.9596050E-03 0.1636848 at 90iterations 2.2730222E-03 0.1093864 at 100iterations 1.4955739E-03 7.2174072E-02 at 110iterations 1.0605364E-03 4.9877167E-02 at 120iterations finished qdiffx linear iterations at : 17:05:12 total time elapsed so far: 8.960000 # loops : 120 mean,max change (kT/e) : 1.0605364E-03 4.9877167E-02 energy calculations done at 8.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.140000 DelPhi exited at 17:05:13 9.142u 0.220s 0:10.02 93.4% 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 17:05:13 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5120 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.271374 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): -14.27100 47.62800 ymin,ymax (A): -28.06900 34.21300 zmin,zma (A): 15.59600 86.12600 x,y,z range (A): 61.89900 62.28200 70.53000 scale (grids/A): 2.271374 object centre (A): 16.67850 3.072001 50.86100 number of atom coordinates read : 5120 total number of charged atoms : 4858 net assigned charge : 8.300034 assigned positive charge : 769.9830 centred at (gu) : 86.25298 90.27792 89.14136 assigned negative charge : -761.6888 centred at (gu) : 86.46564 90.12251 88.99172 start vw surface at 0.2000000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 217116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43580 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 94546 mr = 158618 m= 22651 mr = 72934 m= 3068 mr = 15745 m= 178 mr = 1741 m= 5 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.550000 number of dielectric boundary points 88465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 38765 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) : 1.514249 object centre at (A) : 16.67850 3.072001 50.86100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3721595 0.2321888 midg,1,midg; midg,igrid,midg 8.6472936E-02 4.8064417E-03 1,midg,midg; igrid,midg,midg 0.2479168 -8.4695391E-02 gauss-seidel spectral radius is 0.9991634 estimated iterations to convergence 273 setup time was (sec) 1.880000 now iterating at: 17:05:15 rms-change max change #iterations 10.52791 306.8485 at 10iterations 6.069951 130.0714 at 20iterations 3.462295 85.62809 at 30iterations 1.969628 40.89251 at 40iterations 1.110306 26.11265 at 50iterations 0.6262745 16.07947 at 60iterations 0.3515392 7.600006 at 70iterations 0.1969356 3.706375 at 80iterations 0.1101510 2.313448 at 90iterations 6.1543372E-02 1.245502 at 100iterations 3.4380168E-02 0.6822281 at 110iterations 1.9246871E-02 0.3923988 at 120iterations 1.0779411E-02 0.2080498 at 130iterations 6.0809422E-03 0.1286926 at 140iterations 3.4829215E-03 7.0320129E-02 at 150iterations 2.0468228E-03 4.3014526E-02 at 160iterations 1.2592078E-03 2.9186249E-02 at 170iterations 8.2937267E-04 2.1217346E-02 at 180iterations finished qdiffx linear iterations at : 17:05:26 total time elapsed so far: 12.92000 # loops : 180 mean,max change (kT/e) : 8.2937267E-04 2.1217346E-02 energy calculations done at 12.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 17:05:27 13.094u 0.266s 0:14.09 94.7% 0+0k 0+0io 0pf+0w