Tue Oct 11 03:47:39 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 03:47:39 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6427617 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): -46.19200 1.169000 ymin,ymax (A): -47.35200 1.721000 zmin,zma (A): -9.718000 45.66800 x,y,z range (A): 47.36100 49.07300 55.38600 scale (grids/A): 0.6427617 object centre (A): -22.51150 -22.81550 17.97500 number of atom coordinates read : 2741 total number of charged atoms : 2589 net assigned charge : 4.140018 assigned positive charge : 413.3438 centred at (gu) : 89.87135 90.48559 91.82910 assigned negative charge : -409.2044 centred at (gu) : 89.59266 90.27905 91.79504 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7564 nv = 96 ne = 84 npr = 56322 no. pairs analyzed = 56322 no. exposed pairs = 3256 no. arc points = 22731 no. surface atoms = 1095 nbur = 1646 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 449 mr = 4333 m= 4 mr = 66 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 0.3400000 number of dielectric boundary points 3618 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2247 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9073 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3658343E-09 1.6059964E-08 midg,1,midg; midg,igrid,midg -1.9319730E-08 3.6729602E-08 1,midg,midg; igrid,midg,midg -3.2462864E-08 4.0972676E-08 gauss-seidel spectral radius is 0.9874675 estimated iterations to convergence 73 setup time was (sec) 0.5800000 now iterating at: 03:47:40 rms-change max change #iterations 0.1510032 23.94103 at 10iterations 1.5470515E-02 1.993959 at 20iterations 1.5450966E-03 0.2296028 at 30iterations 1.6138660E-04 2.0511627E-02 at 40iterations 2.0371359E-05 3.1127930E-03 at 50iterations finished qdiffx linear iterations at : 03:47:43 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 2.0371359E-05 3.1127930E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 03:47:43 3.578u 0.218s 0:04.23 89.3% 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 03:47:43 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.928285 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): -46.19200 1.169000 ymin,ymax (A): -47.35200 1.721000 zmin,zma (A): -9.718000 45.66800 x,y,z range (A): 47.36100 49.07300 55.38600 scale (grids/A): 1.928285 object centre (A): -22.51150 -22.81550 17.97500 number of atom coordinates read : 2741 total number of charged atoms : 2589 net assigned charge : 4.140018 assigned positive charge : 413.3438 centred at (gu) : 89.61353 91.45637 95.48663 assigned negative charge : -409.2044 centred at (gu) : 88.77773 90.83667 95.38496 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 81730 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22731 grid for indexing accessible points = 1.400000 m= 31036 mr = 58298 m= 5102 mr = 23453 m= 290 mr = 3258 m= 2 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 973 time to turn everything in is 0.6300000 number of dielectric boundary points 33054 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 167 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20373 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) : 0.6427617 object centre at (A) : -22.51150 -22.81550 17.97500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0763703E-02 1.1921132E-02 midg,1,midg; midg,igrid,midg -1.0571086E-02 3.9554436E-02 1,midg,midg; igrid,midg,midg -1.6144691E-02 5.1693242E-02 gauss-seidel spectral radius is 0.9986792 estimated iterations to convergence 218 setup time was (sec) 0.9400000 now iterating at: 03:47:44 rms-change max change #iterations 4.445161 186.1536 at 10iterations 2.111521 69.45862 at 20iterations 1.006185 31.22357 at 30iterations 0.4791259 13.55315 at 40iterations 0.2271361 7.800288 at 50iterations 0.1078199 3.190845 at 60iterations 5.1361155E-02 1.511879 at 70iterations 2.4382420E-02 0.6823959 at 80iterations 1.1576061E-02 0.3539658 at 90iterations 5.4870797E-03 0.1683769 at 100iterations 2.6025716E-03 7.6720551E-02 at 110iterations 1.2423220E-03 3.7879944E-02 at 120iterations finished qdiffx linear iterations at : 03:47:52 total time elapsed so far: 8.110000 # loops : 120 mean,max change (kT/e) : 1.2423220E-03 3.7879944E-02 energy calculations done at 8.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.290000 DelPhi exited at 03:47:52 8.292u 0.252s 0:08.89 96.0% 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 03:47:52 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.892428 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): -46.19200 1.169000 ymin,ymax (A): -47.35200 1.721000 zmin,zma (A): -9.718000 45.66800 x,y,z range (A): 47.36100 49.07300 55.38600 scale (grids/A): 2.892428 object centre (A): -22.51150 -22.81550 17.97500 number of atom coordinates read : 2741 total number of charged atoms : 2589 net assigned charge : 4.140018 assigned positive charge : 413.3438 centred at (gu) : 89.42010 92.18449 98.22985 assigned negative charge : -409.2044 centred at (gu) : 88.16663 91.25498 98.07726 start vw surface at 0.1900000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 189205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22731 grid for indexing accessible points = 1.400000 m= 100051 mr = 140954 m= 37044 mr = 83234 m= 9157 mr = 30239 m= 1299 mr = 6900 m= 76 mr = 890 m= 0 mr = 20 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 3253 time to turn everything in is 1.640000 number of dielectric boundary points 74595 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 20703 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) : 1.928285 object centre at (A) : -22.51150 -22.81550 17.97500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3034219 0.3938012 midg,1,midg; midg,igrid,midg -0.1391625 0.4411287 1,midg,midg; igrid,midg,midg -0.1276124 0.4117313 gauss-seidel spectral radius is 0.9992664 estimated iterations to convergence 291 setup time was (sec) 1.970000 now iterating at: 03:47:54 rms-change max change #iterations 10.38866 353.4695 at 10iterations 6.085423 129.1333 at 20iterations 3.540448 73.58302 at 30iterations 2.067624 46.05681 at 40iterations 1.198780 24.81738 at 50iterations 0.6957940 12.59371 at 60iterations 0.4019946 7.444091 at 70iterations 0.2328623 4.339569 at 80iterations 0.1346369 2.344524 at 90iterations 7.8021653E-02 1.358855 at 100iterations 4.4965956E-02 0.7789145 at 110iterations 2.5949240E-02 0.4559388 at 120iterations 1.4993438E-02 0.2702179 at 130iterations 8.6661726E-03 0.1478043 at 140iterations 5.0082146E-03 8.0764771E-02 at 150iterations 2.8848792E-03 5.0113678E-02 at 160iterations 1.6685787E-03 2.7957916E-02 at 170iterations 9.6688367E-04 1.6508102E-02 at 180iterations finished qdiffx linear iterations at : 03:48:06 total time elapsed so far: 13.17000 # loops : 180 mean,max change (kT/e) : 9.6688367E-04 1.6508102E-02 energy calculations done at 13.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.37000 DelPhi exited at 03:48:06 13.369u 0.241s 0:14.14 96.1% 0+0k 0+0io 0pf+0w