Sun Oct 9 01:48:18 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+sph2.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 = amb2.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 01:48:18 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3463 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.5475659 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): -40.81000 16.36300 ymin,ymax (A): -12.06800 49.52300 zmin,zma (A): -51.62200 13.39300 x,y,z range (A): 57.17300 61.59100 65.01500 scale (grids/A): 0.5475659 object centre (A): -12.22350 18.72750 -19.11450 number of atom coordinates read : 3463 total number of charged atoms : 3319 net assigned charge : 11.22603 assigned positive charge : 515.3743 centred at (gu) : 89.60529 90.11658 91.59132 assigned negative charge : -504.1501 centred at (gu) : 89.70357 90.04135 91.81646 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6989 nv = 96 ne = 84 npr = 67047 no. pairs analyzed = 67047 no. exposed pairs = 4577 no. arc points = 33498 no. surface atoms = 1533 nbur = 1930 mkacc time = 0.1500000 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 = 1.540000 m= 278 mr = 3479 m= 0 mr = 14 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3774 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3317 ## 405 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9013 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7033456E-09 -1.6290573E-09 midg,1,midg; midg,igrid,midg 1.6340251E-10 1.4054313E-09 1,midg,midg; igrid,midg,midg 1.7031582E-09 -1.5345489E-11 gauss-seidel spectral radius is 0.9828546 estimated iterations to convergence 63 setup time was (sec) 0.5500000 now iterating at: 01:48:19 rms-change max change #iterations 7.9741828E-02 12.68895 at 10iterations 5.3517474E-03 0.7648828 at 20iterations 3.7219241E-04 6.2805176E-02 at 30iterations 3.1060459E-05 3.9577484E-03 at 40iterations 4.0208351E-06 4.1198730E-04 at 50iterations finished qdiffx linear iterations at : 01:48:22 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 4.0208351E-06 4.1198730E-04 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 01:48:22 3.237u 0.190s 0:03.72 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 Sun Oct 9 2011 at 01:48:22 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3463 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.642698 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): -40.81000 16.36300 ymin,ymax (A): -12.06800 49.52300 zmin,zma (A): -51.62200 13.39300 x,y,z range (A): 57.17300 61.59100 65.01500 scale (grids/A): 1.642698 object centre (A): -12.22350 18.72750 -19.11450 number of atom coordinates read : 3463 total number of charged atoms : 3319 net assigned charge : 11.22603 assigned positive charge : 515.3743 centred at (gu) : 88.81461 90.34901 94.77322 assigned negative charge : -504.1501 centred at (gu) : 89.11054 90.12379 95.44917 start vw surface at 0.1900000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 77931 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33498 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23378 mr = 51839 m= 2386 mr = 15688 m= 57 mr = 1106 m= 1 mr = 3 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 909 time to turn everything in is 0.5600000 number of dielectric boundary points 35118 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 355 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 25416 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) : 0.5475659 object centre at (A) : -12.22350 18.72750 -19.11450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7022362E-02 1.2488262E-03 midg,1,midg; midg,igrid,midg 1.5955733E-02 3.2888900E-02 1,midg,midg; igrid,midg,midg 9.0639601E-03 -3.9922381E-03 gauss-seidel spectral radius is 0.9982763 estimated iterations to convergence 191 setup time was (sec) 0.8400000 now iterating at: 01:48:23 rms-change max change #iterations 3.642761 181.6105 at 10iterations 1.543502 57.75108 at 20iterations 0.6575988 24.34723 at 30iterations 0.2798397 9.173614 at 40iterations 0.1192354 3.601318 at 50iterations 5.0844312E-02 1.705144 at 60iterations 2.1523420E-02 0.7303047 at 70iterations 9.2138192E-03 0.3092728 at 80iterations 3.9135604E-03 0.1407204 at 90iterations 1.6761277E-03 5.9628963E-02 at 100iterations 7.1523391E-04 2.5650024E-02 at 110iterations 3.0485445E-04 1.0974884E-02 at 120iterations finished qdiffx linear iterations at : 01:48:30 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 3.0485445E-04 1.0974884E-02 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 01:48:31 7.713u 0.286s 0:08.40 95.1% 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 01:48:31 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3463 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.464047 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): -40.81000 16.36300 ymin,ymax (A): -12.06800 49.52300 zmin,zma (A): -51.62200 13.39300 x,y,z range (A): 57.17300 61.59100 65.01500 scale (grids/A): 2.464047 object centre (A): -12.22350 18.72750 -19.11450 number of atom coordinates read : 3463 total number of charged atoms : 3319 net assigned charge : 11.22603 assigned positive charge : 515.3743 centred at (gu) : 88.22162 90.52321 97.15968 assigned negative charge : -504.1501 centred at (gu) : 88.66579 90.18555 98.17381 start vw surface at 0.1800000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 180950 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33498 grid for indexing accessible points = 1.400000 m= 81404 mr = 127484 m= 22888 mr = 63255 m= 3699 mr = 16857 m= 241 mr = 2328 m= 11 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 2962 time to turn everything in is 1.310000 number of dielectric boundary points 79175 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 26499 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) : 1.642698 object centre at (A) : -12.22350 18.72750 -19.11450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4373215 2.3730155E-02 midg,1,midg; midg,igrid,midg 0.3628102 0.5696967 1,midg,midg; igrid,midg,midg 0.1421830 -3.0786540E-02 gauss-seidel spectral radius is 0.9991873 estimated iterations to convergence 277 setup time was (sec) 1.630000 now iterating at: 01:48:32 rms-change max change #iterations 9.558149 342.9323 at 10iterations 5.506814 137.6075 at 20iterations 3.150846 84.09540 at 30iterations 1.790606 44.50372 at 40iterations 1.014047 24.45894 at 50iterations 0.5720741 14.73656 at 60iterations 0.3219261 6.370042 at 70iterations 0.1811379 3.536449 at 80iterations 0.1016895 2.070450 at 90iterations 5.6993473E-02 1.194131 at 100iterations 3.1940509E-02 0.7974033 at 110iterations 1.7866155E-02 0.3532562 at 120iterations 1.0014940E-02 0.2048988 at 130iterations 5.6051170E-03 0.1178627 at 140iterations 3.1299621E-03 5.7966232E-02 at 150iterations 1.7506181E-03 3.1484127E-02 at 160iterations 9.7914040E-04 1.8451214E-02 at 170iterations 5.4800283E-04 1.0837555E-02 at 180iterations finished qdiffx linear iterations at : 01:48:42 total time elapsed so far: 11.45000 # loops : 180 mean,max change (kT/e) : 5.4800283E-04 1.0837555E-02 energy calculations done at 11.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.62000 DelPhi exited at 01:48:43 11.627u 0.282s 0:12.22 97.3% 0+0k 0+0io 0pf+0w