Sun Oct 9 17:55:31 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 17:55:31 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4847 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5691356 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): 2.873000 64.11400 ymin,ymax (A): -9.426000 52.37100 zmin,zma (A): -2.426000 60.12500 x,y,z range (A): 61.24100 61.79700 62.55100 scale (grids/A): 0.5691356 object centre (A): 33.49350 21.47250 28.84950 number of atom coordinates read : 4847 total number of charged atoms : 4706 net assigned charge : 2.621030 assigned positive charge : 741.6924 centred at (gu) : 88.29582 89.72609 89.90929 assigned negative charge : -739.0766 centred at (gu) : 88.18618 89.75488 89.86483 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 10463 nv = 96 ne = 84 npr = 97546 no. pairs analyzed = 97546 no. exposed pairs = 5704 no. arc points = 38927 no. surface atoms = 1955 nbur = 2892 mkacc time = 0.2200000 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 = 1.512000 m= 500 mr = 6024 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 4905 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4144 ## 481 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 13652 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0335932E-10 1.5256070E-09 midg,1,midg; midg,igrid,midg 1.2455560E-09 -2.6842240E-10 1,midg,midg; igrid,midg,midg -3.6057872E-09 2.1151267E-09 gauss-seidel spectral radius is 0.9842135 estimated iterations to convergence 65 setup time was (sec) 0.7600000 now iterating at: 17:55:32 rms-change max change #iterations 0.1214359 20.82394 at 10iterations 1.1395964E-02 1.720871 at 20iterations 3.1390404E-03 0.3355522 at 30iterations 1.4828461E-03 0.1674147 at 40iterations 7.2991900E-04 8.8259220E-02 at 50iterations finished qdiffx linear iterations at : 17:55:35 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 7.2991900E-04 8.8259220E-02 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.490000 DelPhi exited at 17:55:36 4.489u 0.278s 0:05.08 93.5% 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 17:55:36 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4847 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.707407 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): 2.873000 64.11400 ymin,ymax (A): -9.426000 52.37100 zmin,zma (A): -2.426000 60.12500 x,y,z range (A): 61.24100 61.79700 62.55100 scale (grids/A): 1.707407 object centre (A): 33.49350 21.47250 28.84950 number of atom coordinates read : 4847 total number of charged atoms : 4706 net assigned charge : 2.621030 assigned positive charge : 741.6924 centred at (gu) : 84.88628 89.17712 89.72633 assigned negative charge : -739.0766 centred at (gu) : 84.55834 89.26443 89.59435 start vw surface at 0.2400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 116033 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38927 grid for indexing accessible points = 1.400000 m= 42027 mr = 84508 m= 5512 mr = 30714 m= 207 mr = 2989 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 45537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 370 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 36447 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) : 0.5691356 object centre at (A) : 33.49350 21.47250 28.84950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0498626E-02 -5.1555159E-03 midg,1,midg; midg,igrid,midg 1.7325716E-02 1.4746298E-02 1,midg,midg; igrid,midg,midg 9.0246219E-03 4.0102091E-02 gauss-seidel spectral radius is 0.9985202 estimated iterations to convergence 206 setup time was (sec) 1.300000 now iterating at: 17:55:37 rms-change max change #iterations 4.970793 188.4793 at 10iterations 2.253673 66.89368 at 20iterations 1.024070 26.64167 at 30iterations 0.4661298 14.01512 at 40iterations 0.2128437 6.047572 at 50iterations 9.7281359E-02 2.567039 at 60iterations 4.4753183E-02 1.296131 at 70iterations 2.0961270E-02 0.5353794 at 80iterations 1.0321852E-02 0.2817993 at 90iterations 5.6190449E-03 0.1682549 at 100iterations 3.4943179E-03 9.9510193E-02 at 110iterations 2.4358626E-03 6.0890198E-02 at 120iterations finished qdiffx linear iterations at : 17:55:47 total time elapsed so far: 10.46000 # loops : 120 mean,max change (kT/e) : 2.4358626E-03 6.0890198E-02 energy calculations done at 10.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.64000 DelPhi exited at 17:55:47 10.644u 0.333s 0:11.25 97.5% 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 17:55:47 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4847 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.561110 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): 2.873000 64.11400 ymin,ymax (A): -9.426000 52.37100 zmin,zma (A): -2.426000 60.12500 x,y,z range (A): 61.24100 61.79700 62.55100 scale (grids/A): 2.561110 object centre (A): 33.49350 21.47250 28.84950 number of atom coordinates read : 4847 total number of charged atoms : 4706 net assigned charge : 2.621030 assigned positive charge : 741.6924 centred at (gu) : 82.32899 88.76534 89.58926 assigned negative charge : -739.0766 centred at (gu) : 81.83765 88.89674 89.39149 start vw surface at 0.1900000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 269552 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38927 grid for indexing accessible points = 1.400000 m= 139840 mr = 205142 m= 46586 mr = 114797 m= 9137 mr = 36416 m= 910 mr = 6314 m= 36 mr = 528 m= 0 mr = 9 time to grow re-entrant surface = 1.400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.240000 number of dielectric boundary points 102855 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 2.410000 number of grid points assigned charge 37618 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) : 1.707407 object centre at (A) : 33.49350 21.47250 28.84950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3471564 4.7635236E-03 midg,1,midg; midg,igrid,midg -3.5093229E-03 -2.4347279E-02 1,midg,midg; igrid,midg,midg 0.1736533 0.6276760 gauss-seidel spectral radius is 0.9992749 estimated iterations to convergence 293 setup time was (sec) 2.630000 now iterating at: 17:55:50 rms-change max change #iterations 12.41780 342.1602 at 10iterations 7.396116 149.1111 at 20iterations 4.372857 87.75433 at 30iterations 2.573652 47.92591 at 40iterations 1.508402 25.38902 at 50iterations 0.8822517 16.63967 at 60iterations 0.5157092 8.312090 at 70iterations 0.3000486 4.982072 at 80iterations 0.1745327 2.914316 at 90iterations 0.1016601 1.851982 at 100iterations 5.9264649E-02 0.9357491 at 110iterations 3.4584899E-02 0.5684509 at 120iterations 2.0399595E-02 0.3506737 at 130iterations 1.2243669E-02 0.1903076 at 140iterations 7.5781387E-03 0.1254578 at 150iterations 4.9570361E-03 8.0192566E-02 at 160iterations 3.4837269E-03 6.4758301E-02 at 170iterations 2.6312040E-03 4.3952942E-02 at 180iterations finished qdiffx linear iterations at : 17:56:05 total time elapsed so far: 17.68000 # loops : 180 mean,max change (kT/e) : 2.6312040E-03 4.3952942E-02 energy calculations done at 17.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.86000 DelPhi exited at 17:56:06 17.859u 0.348s 0:18.54 98.1% 0+0k 0+0io 0pf+0w