Mon Oct 10 09:17:03 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 09:17:03 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5941156 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): -35.32200 11.55400 ymin,ymax (A): 1.340000 41.29800 zmin,zma (A): -1.543000 58.37800 x,y,z range (A): 46.87600 39.95800 59.92100 scale (grids/A): 0.5941156 object centre (A): -11.88400 21.31900 28.41750 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 90.03983 89.49810 89.63419 assigned negative charge : -286.4003 centred at (gu) : 89.95586 89.65244 89.64313 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4668 nv = 96 ne = 84 npr = 40200 no. pairs analyzed = 40200 no. exposed pairs = 2505 no. arc points = 17539 no. surface atoms = 856 nbur = 1114 mkacc time = 7.0000008E-02 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= 205 mr = 2464 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2389 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1757 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 5695 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3480744E-09 7.7686174E-10 midg,1,midg; midg,igrid,midg 4.9856994E-09 -2.2010567E-09 1,midg,midg; igrid,midg,midg -8.5016105E-10 2.9322007E-09 gauss-seidel spectral radius is 0.9852869 estimated iterations to convergence 68 setup time was (sec) 0.3400000 now iterating at: 09:17:03 rms-change max change #iterations 8.5289866E-02 16.01875 at 10iterations 7.2135101E-03 1.354414 at 20iterations 5.9859373E-04 0.1097069 at 30iterations 4.7627018E-05 8.6555481E-03 at 40iterations 4.0463647E-06 6.8044662E-04 at 50iterations finished qdiffx linear iterations at : 09:17:06 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 4.0463647E-06 6.8044662E-04 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 09:17:06 3.306u 0.188s 0:03.79 91.8% 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 09:17:06 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.782347 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): -35.32200 11.55400 ymin,ymax (A): 1.340000 41.29800 zmin,zma (A): -1.543000 58.37800 x,y,z range (A): 46.87600 39.95800 59.92100 scale (grids/A): 1.782347 object centre (A): -11.88400 21.31900 28.41750 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 90.11955 88.49448 88.90235 assigned negative charge : -286.4003 centred at (gu) : 89.86771 88.95770 88.92949 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 50307 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17539 grid for indexing accessible points = 1.400000 m= 17314 mr = 33932 m= 2204 mr = 12771 m= 86 mr = 1327 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 371 time to turn everything in is 0.2700000 number of dielectric boundary points 21861 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 14288 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) : 0.5941156 object centre at (A) : -11.88400 21.31900 28.41750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6328167E-02 2.1210527E-02 midg,1,midg; midg,igrid,midg 4.9436581E-03 -6.9752266E-03 1,midg,midg; igrid,midg,midg -1.9324161E-03 -8.6384220E-04 gauss-seidel spectral radius is 0.9983668 estimated iterations to convergence 196 setup time was (sec) 0.4800000 now iterating at: 09:17:07 rms-change max change #iterations 3.120939 181.3287 at 10iterations 1.362792 54.54644 at 20iterations 0.5944542 23.31110 at 30iterations 0.2580927 10.41706 at 40iterations 0.1124043 4.804718 at 50iterations 4.9272571E-02 1.959288 at 60iterations 2.1371756E-02 0.7911789 at 70iterations 9.3018394E-03 0.3632576 at 80iterations 4.0393649E-03 0.1522446 at 90iterations 1.7695675E-03 6.9122314E-02 at 100iterations 7.6907052E-04 2.8405666E-02 at 110iterations 3.3724061E-04 1.3617039E-02 at 120iterations finished qdiffx linear iterations at : 09:17:14 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 3.3724061E-04 1.3617039E-02 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 09:17:15 7.493u 0.183s 0:08.12 94.4% 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 09:17:15 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.673520 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): -35.32200 11.55400 ymin,ymax (A): 1.340000 41.29800 zmin,zma (A): -1.543000 58.37800 x,y,z range (A): 46.87600 39.95800 59.92100 scale (grids/A): 2.673520 object centre (A): -11.88400 21.31900 28.41750 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 90.17924 87.74175 88.35361 assigned negative charge : -286.4003 centred at (gu) : 89.80171 88.43662 88.39425 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 116205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17539 grid for indexing accessible points = 1.400000 m= 57055 mr = 82426 m= 19419 mr = 46400 m= 3817 mr = 15684 m= 382 mr = 2856 m= 13 mr = 220 m= 0 mr = 3 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1150 time to turn everything in is 0.6300000 number of dielectric boundary points 49302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 14701 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) : 1.782347 object centre at (A) : -11.88400 21.31900 28.41750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2160712 0.1237716 midg,1,midg; midg,igrid,midg 1.8463496E-02 -0.1035799 1,midg,midg; igrid,midg,midg -4.5898456E-02 -3.6556497E-02 gauss-seidel spectral radius is 0.9991630 estimated iterations to convergence 273 setup time was (sec) 0.8500000 now iterating at: 09:17:16 rms-change max change #iterations 7.586649 278.2611 at 10iterations 4.234744 154.0389 at 20iterations 2.365544 62.09090 at 30iterations 1.310041 28.82735 at 40iterations 0.7258546 15.83598 at 50iterations 0.4015078 9.160675 at 60iterations 0.2219945 4.579019 at 70iterations 0.1229037 2.717228 at 80iterations 6.7901716E-02 1.504776 at 90iterations 3.7651144E-02 0.8751585 at 100iterations 2.0831233E-02 0.4363632 at 110iterations 1.1514531E-02 0.2737312 at 120iterations 6.3523906E-03 0.1602407 at 130iterations 3.5113308E-03 7.6489449E-02 at 140iterations 1.9426887E-03 4.8023701E-02 at 150iterations 1.0780441E-03 2.2618055E-02 at 160iterations 5.9425068E-04 1.2414932E-02 at 170iterations 3.2815291E-04 7.2016716E-03 at 180iterations finished qdiffx linear iterations at : 09:17:26 total time elapsed so far: 11.74000 # loops : 180 mean,max change (kT/e) : 3.2815291E-04 7.2016716E-03 energy calculations done at 11.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.86000 DelPhi exited at 09:17:27 11.867u 0.220s 0:12.68 95.2% 0+0k 0+0io 0pf+0w