Sun Oct 9 07:23:29 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 Sun Oct 9 2011 at 07:23:29 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 = 1571 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7639649 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): -6.549000 35.24800 ymin,ymax (A): -2.310000 39.95400 zmin,zma (A): -13.35600 33.24300 x,y,z range (A): 41.79700 42.26400 46.59900 scale (grids/A): 0.7639649 object centre (A): 14.34950 18.82200 9.943501 number of atom coordinates read : 1571 total number of charged atoms : 1434 net assigned charge : -7.999991 assigned positive charge : 227.5042 centred at (gu) : 90.51807 89.26831 90.97818 assigned negative charge : -235.5041 centred at (gu) : 90.32700 89.67664 91.11897 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6506 nv = 96 ne = 84 npr = 32102 no. pairs analyzed = 32102 no. exposed pairs = 2108 no. arc points = 15022 no. surface atoms = 717 nbur = 854 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 489 mr = 3529 m= 9 mr = 109 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1086 ## 75 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6354 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9221502E-08 -4.8469838E-07 midg,1,midg; midg,igrid,midg 2.7346334E-07 -6.5079263E-07 1,midg,midg; igrid,midg,midg -4.2644515E-07 -9.3192289E-09 gauss-seidel spectral radius is 0.9910176 estimated iterations to convergence 86 setup time was (sec) 0.6000000 now iterating at: 07:23:30 rms-change max change #iterations 0.2361328 39.26370 at 10iterations 3.3511017E-02 4.720306 at 20iterations 4.7186096E-03 0.9182463 at 30iterations 6.7912601E-04 9.5043182E-02 at 40iterations 9.7253593E-05 1.5182495E-02 at 50iterations finished qdiffx linear iterations at : 07:23:33 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 9.7253593E-05 1.5182495E-02 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 07:23:34 4.246u 0.232s 0:04.80 93.1% 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 Sun Oct 9 2011 at 07:23:34 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 = 1571 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.291895 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): -6.549000 35.24800 ymin,ymax (A): -2.310000 39.95400 zmin,zma (A): -13.35600 33.24300 x,y,z range (A): 41.79700 42.26400 46.59900 scale (grids/A): 2.291895 object centre (A): 14.34950 18.82200 9.943501 number of atom coordinates read : 1571 total number of charged atoms : 1434 net assigned charge : -7.999991 assigned positive charge : 227.5042 centred at (gu) : 91.55418 87.80530 92.93470 assigned negative charge : -235.5041 centred at (gu) : 90.98105 89.02982 93.35712 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 67212 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15022 grid for indexing accessible points = 1.400000 m= 28370 mr = 45109 m= 6653 mr = 21950 m= 732 mr = 4665 m= 27 mr = 450 m= 1 mr = 4 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 30818 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 11435 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) : 0.7639649 object centre at (A) : 14.34950 18.82200 9.943501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9701382E-02 -6.1432522E-02 midg,1,midg; midg,igrid,midg 1.2975751E-02 -0.1165584 1,midg,midg; igrid,midg,midg -7.8442067E-02 -2.3107825E-02 gauss-seidel spectral radius is 0.9989406 estimated iterations to convergence 243 setup time was (sec) 1.080000 now iterating at: 07:23:35 rms-change max change #iterations 4.569499 204.0170 at 10iterations 2.345027 100.8992 at 20iterations 1.196360 36.69258 at 30iterations 0.6158277 20.15002 at 40iterations 0.3157526 9.497656 at 50iterations 0.1619796 5.212720 at 60iterations 8.3223335E-02 2.478600 at 70iterations 4.2658474E-02 1.394534 at 80iterations 2.1872286E-02 0.7069426 at 90iterations 1.1227611E-02 0.3304405 at 100iterations 5.7254061E-03 0.1696215 at 110iterations 2.9331441E-03 9.2914581E-02 at 120iterations finished qdiffx linear iterations at : 07:23:44 total time elapsed so far: 9.660000 # loops : 120 mean,max change (kT/e) : 2.9331441E-03 9.2914581E-02 energy calculations done at 9.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.900000 DelPhi exited at 07:23:44 9.900u 0.251s 0:10.42 97.4% 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 Sun Oct 9 2011 at 07:23:44 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 = 1571 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.437842 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): -6.549000 35.24800 ymin,ymax (A): -2.310000 39.95400 zmin,zma (A): -13.35600 33.24300 x,y,z range (A): 41.79700 42.26400 46.59900 scale (grids/A): 3.437842 object centre (A): 14.34950 18.82200 9.943501 number of atom coordinates read : 1571 total number of charged atoms : 1434 net assigned charge : -7.999991 assigned positive charge : 227.5042 centred at (gu) : 92.33136 86.70790 94.40213 assigned negative charge : -235.5041 centred at (gu) : 91.47161 88.54486 95.03570 start vw surface at 0.1600000 fill in re-entrant regions at 0.9900000 boundary points on vw surface= 154296 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15022 grid for indexing accessible points = 1.400000 m= 84025 mr = 108669 m= 39253 mr = 69701 m= 12954 mr = 33163 m= 3051 mr = 10462 m= 444 mr = 2328 m= 34 mr = 322 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.210000 number of dielectric boundary points 69394 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.390000 number of grid points assigned charge 11472 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) : 2.291895 object centre at (A) : 14.34950 18.82200 9.943501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2861941 -0.9618583 midg,1,midg; midg,igrid,midg 0.1902488 -0.6992232 1,midg,midg; igrid,midg,midg -0.4765667 -0.1025706 gauss-seidel spectral radius is 0.9993276 estimated iterations to convergence 304 setup time was (sec) 2.610000 now iterating at: 07:23:47 rms-change max change #iterations 9.920225 289.2245 at 10iterations 5.911050 135.6881 at 20iterations 3.522945 67.95586 at 30iterations 2.093799 40.38853 at 40iterations 1.244504 24.26722 at 50iterations 0.7346176 12.76804 at 60iterations 0.4346501 8.006157 at 70iterations 0.2577935 5.545938 at 80iterations 0.1520238 2.717605 at 90iterations 8.9969866E-02 1.724125 at 100iterations 5.3159758E-02 1.057011 at 110iterations 3.1245092E-02 0.6302662 at 120iterations 1.8485229E-02 0.3041210 at 130iterations 1.0902153E-02 0.1892707 at 140iterations 6.4297174E-03 0.1233263 at 150iterations 3.8028769E-03 6.5322876E-02 at 160iterations 2.2450839E-03 3.9337635E-02 at 170iterations 1.3242612E-03 2.4491787E-02 at 180iterations finished qdiffx linear iterations at : 07:24:01 total time elapsed so far: 16.10000 # loops : 180 mean,max change (kT/e) : 1.3242612E-03 2.4491787E-02 energy calculations done at 16.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.35000 DelPhi exited at 07:24:01 16.349u 0.276s 0:16.99 97.7% 0+0k 0+0io 0pf+0w