Sat Oct 8 16:42:59 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 Sat Oct 8 2011 at 16:42:59 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4553 !!! WARNING: FAD 994 has a net charge of -2.0000 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: 0.5417086 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): 17.18500 79.93900 ymin,ymax (A): 117.1770 182.8950 zmin,zma (A): -1.257000 60.31300 x,y,z range (A): 62.75400 65.71799 61.57000 scale (grids/A): 0.5417086 object centre (A): 48.56200 150.0360 29.52800 number of atom coordinates read : 4553 total number of charged atoms : 4378 net assigned charge : 3.000041 assigned positive charge : 699.2747 centred at (gu) : 92.17000 89.41734 87.27981 assigned negative charge : -696.2781 centred at (gu) : 92.12428 89.33471 87.29702 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8648 nv = 96 ne = 84 npr = 91010 no. pairs analyzed = 91010 no. exposed pairs = 5442 no. arc points = 38231 no. surface atoms = 1827 nbur = 2726 mkacc time = 0.2500000 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= 345 mr = 4652 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.5200000 number of dielectric boundary points 4320 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3974 ## 545 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 11409 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8616351E-10 2.7201654E-13 midg,1,midg; midg,igrid,midg -6.7611305E-10 7.4222184E-10 1,midg,midg; igrid,midg,midg -1.4577634E-10 9.3987584E-10 gauss-seidel spectral radius is 0.9825525 estimated iterations to convergence 62 setup time was (sec) 0.8000000 now iterating at: 16:43:00 rms-change max change #iterations 9.0098470E-02 21.91678 at 10iterations 5.9827380E-03 0.8144417 at 20iterations 5.4021931E-04 7.8982353E-02 at 30iterations 1.1264542E-04 1.8809319E-02 at 40iterations 3.3237156E-05 5.8922768E-03 at 50iterations finished qdiffx linear iterations at : 16:43:03 total time elapsed so far: 4.190000 # loops : 50 mean,max change (kT/e) : 3.3237156E-05 5.8922768E-03 energy calculations done at 4.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 16:43:04 4.373u 0.291s 0:04.94 94.3% 0+0k 0+0io 6pf+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 Sat Oct 8 2011 at 16:43:04 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4553 !!! WARNING: FAD 994 has a net charge of -2.0000 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: 1.625126 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): 17.18500 79.93900 ymin,ymax (A): 117.1770 182.8950 zmin,zma (A): -1.257000 60.31300 x,y,z range (A): 62.75400 65.71799 61.57000 scale (grids/A): 1.625126 object centre (A): 48.56200 150.0360 29.52800 number of atom coordinates read : 4553 total number of charged atoms : 4378 net assigned charge : 3.000041 assigned positive charge : 699.2747 centred at (gu) : 96.50851 88.25085 81.83836 assigned negative charge : -696.2781 centred at (gu) : 96.37243 88.00388 81.89079 start vw surface at 0.2000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 96809 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38231 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 31180 mr = 67724 m= 3585 mr = 22008 m= 97 mr = 1953 m= 0 mr = 8 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 965 time to turn everything in is 0.8400000 number of dielectric boundary points 39978 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 490 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 33523 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) : 0.5417086 object centre at (A) : 48.56200 150.0360 29.52800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9466530E-03 7.8171743E-03 midg,1,midg; midg,igrid,midg 1.2014877E-02 3.4081120E-02 1,midg,midg; igrid,midg,midg -1.0376463E-02 -1.6860884E-02 gauss-seidel spectral radius is 0.9983174 estimated iterations to convergence 194 setup time was (sec) 1.130000 now iterating at: 16:43:05 rms-change max change #iterations 4.286355 258.9352 at 10iterations 1.836216 90.36266 at 20iterations 0.7903111 34.85145 at 30iterations 0.3402522 11.95823 at 40iterations 0.1469454 4.865741 at 50iterations 6.3280016E-02 2.072433 at 60iterations 2.7361127E-02 0.8437805 at 70iterations 1.1837068E-02 0.3593464 at 80iterations 5.1191477E-03 0.1515884 at 90iterations 2.2321581E-03 6.7827225E-02 at 100iterations 9.7361743E-04 2.9445648E-02 at 110iterations 4.3155078E-04 1.2588501E-02 at 120iterations finished qdiffx linear iterations at : 16:43:14 total time elapsed so far: 9.870000 # loops : 120 mean,max change (kT/e) : 4.3155078E-04 1.2588501E-02 energy calculations done at 9.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.06000 DelPhi exited at 16:43:14 10.061u 0.351s 0:10.69 97.3% 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 Sat Oct 8 2011 at 16:43:14 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4553 !!! WARNING: FAD 994 has a net charge of -2.0000 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: 2.437689 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): 17.18500 79.93900 ymin,ymax (A): 117.1770 182.8950 zmin,zma (A): -1.257000 60.31300 x,y,z range (A): 62.75400 65.71799 61.57000 scale (grids/A): 2.437689 object centre (A): 48.56200 150.0360 29.52800 number of atom coordinates read : 4553 total number of charged atoms : 4378 net assigned charge : 3.000041 assigned positive charge : 699.2747 centred at (gu) : 99.76266 87.37598 77.75716 assigned negative charge : -696.2781 centred at (gu) : 99.55869 87.00587 77.83620 start vw surface at 0.2000000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 225292 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38231 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 107413 mr = 165537 m= 31806 mr = 86303 m= 5805 mr = 24322 m= 450 mr = 4095 m= 2 mr = 194 m= 0 mr = 0 time to grow re-entrant surface = 1.280000 no. cavity mid-points inaccessible to solvent = 3404 time to turn everything in is 2.090000 number of dielectric boundary points 90317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 34983 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) : 1.625126 object centre at (A) : 48.56200 150.0360 29.52800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1920706E-02 0.1676184 midg,1,midg; midg,igrid,midg 0.2288616 0.6717733 1,midg,midg; igrid,midg,midg -0.1532593 -0.3332182 gauss-seidel spectral radius is 0.9992083 estimated iterations to convergence 281 setup time was (sec) 2.440000 now iterating at: 16:43:17 rms-change max change #iterations 10.98521 487.8306 at 10iterations 6.323713 152.1398 at 20iterations 3.614801 73.27800 at 30iterations 2.063820 41.55121 at 40iterations 1.174184 23.04877 at 50iterations 0.6662937 11.78331 at 60iterations 0.3772576 6.911526 at 70iterations 0.2133231 3.797409 at 80iterations 0.1206433 2.017265 at 90iterations 6.8235524E-02 1.155927 at 100iterations 3.8515519E-02 0.6386724 at 110iterations 2.1751394E-02 0.3773651 at 120iterations 1.2280813E-02 0.2024002 at 130iterations 6.9266292E-03 0.1190972 at 140iterations 3.9107199E-03 7.1584702E-02 at 150iterations 2.2035195E-03 3.8111687E-02 at 160iterations 1.2420595E-03 2.4389029E-02 at 170iterations 7.0182566E-04 1.4686584E-02 at 180iterations finished qdiffx linear iterations at : 16:43:32 total time elapsed so far: 17.24000 # loops : 180 mean,max change (kT/e) : 7.0182566E-04 1.4686584E-02 energy calculations done at 17.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.43000 DelPhi exited at 16:43:32 17.430u 0.357s 0:18.05 98.5% 0+0k 0+0io 0pf+0w