Mon Oct 10 17:16:24 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 17:16:24 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 = 4795 !!! 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: 0.5132346 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): -17.91800 36.85600 ymin,ymax (A): -30.68300 34.05000 zmin,zma (A): -3.864000 65.50000 x,y,z range (A): 54.77400 64.73300 69.36400 scale (grids/A): 0.5132346 object centre (A): 9.469002 1.683501 30.81800 number of atom coordinates read : 4795 total number of charged atoms : 4549 net assigned charge : 7.800032 assigned positive charge : 719.8364 centred at (gu) : 90.20820 90.46662 88.39978 assigned negative charge : -712.0408 centred at (gu) : 90.09360 90.52338 88.36359 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8095 nv = 96 ne = 84 npr = 96349 no. pairs analyzed = 96349 no. exposed pairs = 6159 no. arc points = 42970 no. surface atoms = 2053 nbur = 2742 mkacc time = 0.1700000 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 = 1.652000 m= 289 mr = 4168 m= 0 mr = 5 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4211 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4117 ## 604 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 10682 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9217392E-11 1.5236992E-10 midg,1,midg; midg,igrid,midg 2.5563771E-10 -4.4616179E-11 1,midg,midg; igrid,midg,midg -1.9775692E-10 4.7717735E-10 gauss-seidel spectral radius is 0.9805890 estimated iterations to convergence 59 setup time was (sec) 0.5000000 now iterating at: 17:16:24 rms-change max change #iterations 6.9603734E-02 11.84831 at 10iterations 4.1479515E-03 0.6474876 at 20iterations 4.3182474E-04 5.9854507E-02 at 30iterations 1.4019350E-04 2.3015976E-02 at 40iterations 5.6180157E-05 1.0270596E-02 at 50iterations finished qdiffx linear iterations at : 17:16:27 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 5.6180157E-05 1.0270596E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 17:16:28 3.468u 0.181s 0:03.96 91.9% 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 17:16:28 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 = 4795 !!! 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: 1.539704 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): -17.91800 36.85600 ymin,ymax (A): -30.68300 34.05000 zmin,zma (A): -3.864000 65.50000 x,y,z range (A): 54.77400 64.73300 69.36400 scale (grids/A): 1.539704 object centre (A): 9.469002 1.683501 30.81800 number of atom coordinates read : 4795 total number of charged atoms : 4549 net assigned charge : 7.800032 assigned positive charge : 719.8364 centred at (gu) : 90.62305 91.39847 85.19798 assigned negative charge : -712.0408 centred at (gu) : 90.28072 91.57014 85.09044 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 91533 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42970 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26439 mr = 62658 m= 2270 mr = 17404 m= 44 mr = 879 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 0.4300000 number of dielectric boundary points 39344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 568 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 34309 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) : 0.5132346 object centre at (A) : 9.469002 1.683501 30.81800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8462790E-03 2.2316087E-02 midg,1,midg; midg,igrid,midg 1.0616282E-02 -1.3038811E-02 1,midg,midg; igrid,midg,midg -1.2892799E-03 1.1586842E-02 gauss-seidel spectral radius is 0.9981425 estimated iterations to convergence 184 setup time was (sec) 0.6500000 now iterating at: 17:16:29 rms-change max change #iterations 3.841582 175.5349 at 10iterations 1.579704 63.47726 at 20iterations 0.6547625 21.05153 at 30iterations 0.2704962 8.724240 at 40iterations 0.1120034 3.551739 at 50iterations 4.6419580E-02 1.633035 at 60iterations 1.9190950E-02 0.6356163 at 70iterations 7.9551870E-03 0.2486744 at 80iterations 3.3077172E-03 0.1087456 at 90iterations 1.3864138E-03 4.5053482E-02 at 100iterations 5.9476332E-04 2.2415638E-02 at 110iterations 2.7039877E-04 1.0204315E-02 at 120iterations finished qdiffx linear iterations at : 17:16:36 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 2.7039877E-04 1.0204315E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 17:16:36 7.811u 0.205s 0:08.36 95.8% 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 17:16:36 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 = 4795 !!! 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: 2.309556 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): -17.91800 36.85600 ymin,ymax (A): -30.68300 34.05000 zmin,zma (A): -3.864000 65.50000 x,y,z range (A): 54.77400 64.73300 69.36400 scale (grids/A): 2.309556 object centre (A): 9.469002 1.683501 30.81800 number of atom coordinates read : 4795 total number of charged atoms : 4549 net assigned charge : 7.800032 assigned positive charge : 719.8364 centred at (gu) : 90.93428 92.09734 82.79668 assigned negative charge : -712.0408 centred at (gu) : 90.42093 92.35493 82.63564 start vw surface at 0.1300000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 213260 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42970 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 95113 mr = 154329 m= 23847 mr = 73921 m= 3157 mr = 16639 m= 149 mr = 1825 m= 0 mr = 43 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.070000 number of dielectric boundary points 88769 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 36313 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) : 1.539704 object centre at (A) : 9.469002 1.683501 30.81800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8299131E-02 0.5214739 midg,1,midg; midg,igrid,midg 0.2437881 -0.2917988 1,midg,midg; igrid,midg,midg -1.3683143E-02 0.1665549 gauss-seidel spectral radius is 0.9991769 estimated iterations to convergence 275 setup time was (sec) 1.300000 now iterating at: 17:16:38 rms-change max change #iterations 10.40163 285.5466 at 10iterations 5.992267 163.6970 at 20iterations 3.429171 89.90172 at 30iterations 1.955077 42.38043 at 40iterations 1.106977 25.16174 at 50iterations 0.6245682 14.40362 at 60iterations 0.3518002 6.971746 at 70iterations 0.1981993 4.097761 at 80iterations 0.1111295 2.272453 at 90iterations 6.2283341E-02 1.309689 at 100iterations 3.4904860E-02 0.6697235 at 110iterations 1.9573169E-02 0.3936768 at 120iterations 1.0947410E-02 0.2194901 at 130iterations 6.1268532E-03 0.1400566 at 140iterations 3.4226025E-03 6.4053059E-02 at 150iterations 1.9205182E-03 4.1880131E-02 at 160iterations 1.0823414E-03 2.0042300E-02 at 170iterations 6.1246194E-04 1.1527808E-02 at 180iterations finished qdiffx linear iterations at : 17:16:49 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 6.1246194E-04 1.1527808E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 17:16:50 12.888u 0.216s 0:13.40 97.6% 0+0k 0+0io 0pf+0w