Mon Oct 10 17:00:22 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 17:00:22 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4656 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5100725 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): -18.68100 37.22500 ymin,ymax (A): -30.88800 34.13800 zmin,zma (A): -3.970000 65.82400 x,y,z range (A): 55.90600 65.02600 69.79400 scale (grids/A): 0.5100725 object centre (A): 9.272001 1.625000 30.92700 number of atom coordinates read : 4656 total number of charged atoms : 4411 net assigned charge : 5.800023 assigned positive charge : 697.8276 centred at (gu) : 90.20086 90.42126 88.25919 assigned negative charge : -692.0320 centred at (gu) : 90.08498 90.43882 88.23714 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7789 nv = 96 ne = 84 npr = 93322 no. pairs analyzed = 93322 no. exposed pairs = 6032 no. arc points = 41779 no. surface atoms = 2012 nbur = 2644 mkacc time = 0.1600000 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= 268 mr = 3991 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4066 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3989 ## 571 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 10237 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.0150945E-11 8.5913221E-11 midg,1,midg; midg,igrid,midg 1.1091750E-10 4.1853767E-11 1,midg,midg; igrid,midg,midg -1.9628053E-10 3.7994619E-10 gauss-seidel spectral radius is 0.9803399 estimated iterations to convergence 59 setup time was (sec) 0.5100000 now iterating at: 17:00:23 rms-change max change #iterations 6.6127196E-02 9.398741 at 10iterations 3.9396891E-03 0.6618080 at 20iterations 4.9131655E-04 6.7226410E-02 at 30iterations 1.8561103E-04 2.7324438E-02 at 40iterations 8.0232749E-05 1.2309313E-02 at 50iterations finished qdiffx linear iterations at : 17:00:26 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 8.0232749E-05 1.2309313E-02 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 17:00:26 3.553u 0.182s 0:04.38 85.1% 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 Mon Oct 10 2011 at 17:00:27 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4656 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.530218 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): -18.68100 37.22500 ymin,ymax (A): -30.88800 34.13800 zmin,zma (A): -3.970000 65.82400 x,y,z range (A): 55.90600 65.02600 69.79400 scale (grids/A): 1.530218 object centre (A): 9.272001 1.625000 30.92700 number of atom coordinates read : 4656 total number of charged atoms : 4411 net assigned charge : 5.800023 assigned positive charge : 697.8276 centred at (gu) : 90.60128 91.26231 84.77624 assigned negative charge : -692.0320 centred at (gu) : 90.25481 91.31615 84.71122 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 88280 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41779 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25310 mr = 60452 m= 2149 mr = 16580 m= 34 mr = 867 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 37873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 575 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 33088 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) : 0.5100725 object centre at (A) : 9.272001 1.625000 30.92700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6156045E-03 1.8605620E-02 midg,1,midg; midg,igrid,midg 2.8507377E-03 -7.5463299E-03 1,midg,midg; igrid,midg,midg -1.7689932E-03 1.1351406E-02 gauss-seidel spectral radius is 0.9981027 estimated iterations to convergence 182 setup time was (sec) 0.6600000 now iterating at: 17:00:27 rms-change max change #iterations 3.723725 175.6860 at 10iterations 1.522942 52.23523 at 20iterations 0.6233526 22.05862 at 30iterations 0.2560529 8.967930 at 40iterations 0.1048283 3.456032 at 50iterations 4.2927656E-02 1.316610 at 60iterations 1.7582346E-02 0.5574703 at 70iterations 7.2504901E-03 0.2240219 at 80iterations 2.9908407E-03 9.9433899E-02 at 90iterations 1.2469619E-03 3.7087440E-02 at 100iterations 5.3417846E-04 1.8918991E-02 at 110iterations 2.4735869E-04 9.7002983E-03 at 120iterations finished qdiffx linear iterations at : 17:00:35 total time elapsed so far: 8.280000 # loops : 120 mean,max change (kT/e) : 2.4735869E-04 9.7002983E-03 energy calculations done at 8.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.400000 DelPhi exited at 17:00:36 8.407u 0.249s 0:09.51 90.8% 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 17:00:36 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4656 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.295326 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): -18.68100 37.22500 ymin,ymax (A): -30.88800 34.13800 zmin,zma (A): -3.970000 65.82400 x,y,z range (A): 55.90600 65.02600 69.79400 scale (grids/A): 2.295326 object centre (A): 9.272001 1.625000 30.92700 number of atom coordinates read : 4656 total number of charged atoms : 4411 net assigned charge : 5.800023 assigned positive charge : 697.8276 centred at (gu) : 90.90136 91.89310 82.16407 assigned negative charge : -692.0320 centred at (gu) : 90.38219 91.97406 82.06682 start vw surface at 0.1200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 205558 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41779 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 91425 mr = 148468 m= 22545 mr = 70919 m= 3100 mr = 15893 m= 164 mr = 1878 m= 1 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.050000 number of dielectric boundary points 85572 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 35189 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) : 1.530218 object centre at (A) : 9.272001 1.625000 30.92700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1277926 0.4803388 midg,1,midg; midg,igrid,midg -1.9898066E-02 -0.2139048 1,midg,midg; igrid,midg,midg -2.1890452E-02 0.1603084 gauss-seidel spectral radius is 0.9991592 estimated iterations to convergence 272 setup time was (sec) 1.300000 now iterating at: 17:00:38 rms-change max change #iterations 10.17111 305.8221 at 10iterations 5.826689 147.0904 at 20iterations 3.316487 80.14781 at 30iterations 1.870087 56.27253 at 40iterations 1.054257 24.07480 at 50iterations 0.5908279 13.41507 at 60iterations 0.3305359 6.845735 at 70iterations 0.1852371 4.011177 at 80iterations 0.1032218 2.199631 at 90iterations 5.7473522E-02 1.216782 at 100iterations 3.2021020E-02 0.5890446 at 110iterations 1.7830115E-02 0.3735771 at 120iterations 9.9054454E-03 0.2192678 at 130iterations 5.5282032E-03 0.1027451 at 140iterations 3.0773962E-03 6.0985565E-02 at 150iterations 1.7258876E-03 3.5440445E-02 at 160iterations 9.7780838E-04 2.2117615E-02 at 170iterations 5.6433649E-04 1.1294603E-02 at 180iterations finished qdiffx linear iterations at : 17:00:50 total time elapsed so far: 13.16000 # loops : 180 mean,max change (kT/e) : 5.6433649E-04 1.1294603E-02 energy calculations done at 13.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.29000 DelPhi exited at 17:00:50 13.293u 0.278s 0:14.08 96.3% 0+0k 0+0io 0pf+0w