Tue Oct 11 08:05:40 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 Tue Oct 11 2011 at 08:05:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3012 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5494336 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): -21.05500 43.01100 ymin,ymax (A): -1.735000 63.05900 zmin,zma (A): 7.173000 54.72100 x,y,z range (A): 64.06600 64.79400 47.54800 scale (grids/A): 0.5494336 object centre (A): 10.97800 30.66200 30.94700 number of atom coordinates read : 3012 total number of charged atoms : 2867 net assigned charge : 8.500025 assigned positive charge : 444.5080 centred at (gu) : 89.87225 90.60677 89.89782 assigned negative charge : -436.0091 centred at (gu) : 89.74108 90.64786 89.91462 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6201 nv = 96 ne = 84 npr = 56652 no. pairs analyzed = 56652 no. exposed pairs = 4308 no. arc points = 31054 no. surface atoms = 1438 nbur = 1574 mkacc time = 0.1300000 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 = 1.568000 m= 229 mr = 2863 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3567 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3150 ## 422 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7965 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5216483E-10 4.7326126E-10 midg,1,midg; midg,igrid,midg 7.8813051E-10 3.4834893E-10 1,midg,midg; igrid,midg,midg -3.9222967E-10 1.5178128E-09 gauss-seidel spectral radius is 0.9829413 estimated iterations to convergence 63 setup time was (sec) 0.5300000 now iterating at: 08:05:40 rms-change max change #iterations 7.3171660E-02 12.80322 at 10iterations 4.8452294E-03 0.9142036 at 20iterations 3.2094633E-04 5.0050735E-02 at 30iterations 2.2712602E-05 3.7851334E-03 at 40iterations 1.7324669E-06 2.5367737E-04 at 50iterations finished qdiffx linear iterations at : 08:05:43 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 1.7324669E-06 2.5367737E-04 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 08:05:44 3.109u 0.142s 0:03.91 82.8% 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 Tue Oct 11 2011 at 08:05:44 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3012 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.648301 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): -21.05500 43.01100 ymin,ymax (A): -1.735000 63.05900 zmin,zma (A): 7.173000 54.72100 x,y,z range (A): 64.06600 64.79400 47.54800 scale (grids/A): 1.648301 object centre (A): 10.97800 30.66200 30.94700 number of atom coordinates read : 3012 total number of charged atoms : 2867 net assigned charge : 8.500025 assigned positive charge : 444.5080 centred at (gu) : 89.61585 91.81951 89.69231 assigned negative charge : -436.0091 centred at (gu) : 89.22263 91.94328 89.74355 start vw surface at 0.2300000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 67914 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31054 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19376 mr = 42859 m= 1911 mr = 12386 m= 51 mr = 830 m= 0 mr = 4 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 80 time to turn everything in is 0.5500000 number of dielectric boundary points 33173 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 337 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 22006 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) : 0.5494336 object centre at (A) : 10.97800 30.66200 30.94700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2418235E-03 8.1804283E-03 midg,1,midg; midg,igrid,midg -6.7401137E-03 -1.6406359E-02 1,midg,midg; igrid,midg,midg 9.3873972E-03 3.0107288E-02 gauss-seidel spectral radius is 0.9982445 estimated iterations to convergence 190 setup time was (sec) 0.8000000 now iterating at: 08:05:45 rms-change max change #iterations 3.368278 198.6772 at 10iterations 1.409717 82.09644 at 20iterations 0.5929540 30.78648 at 30iterations 0.2487866 9.603577 at 40iterations 0.1054268 3.708358 at 50iterations 4.4403672E-02 1.579494 at 60iterations 1.8675629E-02 0.6362762 at 70iterations 7.9107974E-03 0.2956219 at 80iterations 3.3304144E-03 0.1216297 at 90iterations 1.4064563E-03 4.9695015E-02 at 100iterations 5.9322262E-04 2.1608353E-02 at 110iterations 2.5047129E-04 1.0339737E-02 at 120iterations finished qdiffx linear iterations at : 08:05:50 total time elapsed so far: 6.670000 # loops : 120 mean,max change (kT/e) : 2.5047129E-04 1.0339737E-02 energy calculations done at 6.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.850000 DelPhi exited at 08:05:51 6.857u 0.178s 0:07.42 94.6% 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 Tue Oct 11 2011 at 08:05:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3012 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.472451 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): -21.05500 43.01100 ymin,ymax (A): -1.735000 63.05900 zmin,zma (A): 7.173000 54.72100 x,y,z range (A): 64.06600 64.79400 47.54800 scale (grids/A): 2.472451 object centre (A): 10.97800 30.66200 30.94700 number of atom coordinates read : 3012 total number of charged atoms : 2867 net assigned charge : 8.500025 assigned positive charge : 444.5080 centred at (gu) : 89.42358 92.72892 89.53831 assigned negative charge : -436.0091 centred at (gu) : 88.83388 92.91479 89.61534 start vw surface at 0.2300000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 157717 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31054 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67141 mr = 105729 m= 18146 mr = 50999 m= 2745 mr = 12809 m= 212 mr = 1656 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 236 time to turn everything in is 1.180000 number of dielectric boundary points 74700 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 22916 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) : 1.648301 object centre at (A) : 10.97800 30.66200 30.94700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9549059E-02 0.1138127 midg,1,midg; midg,igrid,midg -0.1241660 -0.1407167 1,midg,midg; igrid,midg,midg 0.1476325 0.3970545 gauss-seidel spectral radius is 0.9991691 estimated iterations to convergence 274 setup time was (sec) 1.450000 now iterating at: 08:05:53 rms-change max change #iterations 8.760093 327.0293 at 10iterations 5.009972 133.1326 at 20iterations 2.848049 67.08952 at 30iterations 1.602618 45.97967 at 40iterations 0.9003099 19.86158 at 50iterations 0.5038984 11.06142 at 60iterations 0.2819492 5.923294 at 70iterations 0.1572384 3.267303 at 80iterations 8.7584272E-02 1.859917 at 90iterations 4.8887469E-02 1.142807 at 100iterations 2.7124979E-02 0.6072197 at 110iterations 1.5061851E-02 0.3463392 at 120iterations 8.3703762E-03 0.1718731 at 130iterations 4.6626623E-03 0.1041784 at 140iterations 2.5784601E-03 5.1177025E-02 at 150iterations 1.4307090E-03 2.9337808E-02 at 160iterations 7.9582614E-04 1.5443802E-02 at 170iterations 4.4233643E-04 9.7503662E-03 at 180iterations finished qdiffx linear iterations at : 08:06:02 total time elapsed so far: 10.95000 # loops : 180 mean,max change (kT/e) : 4.4233643E-04 9.7503662E-03 energy calculations done at 10.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.12000 DelPhi exited at 08:06:03 11.128u 0.157s 0:11.60 97.1% 0+0k 0+0io 0pf+0w