Sun Oct 9 08:56:41 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 08:56:41 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5497 !!! WARNING: HIR 702 has a net charge of 0.5140 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: 0.5009568 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): 3.845000 74.90900 ymin,ymax (A): 22.52600 84.18800 zmin,zma (A): 6.300000 70.56900 x,y,z range (A): 71.06400 61.66199 64.26900 scale (grids/A): 0.5009568 object centre (A): 39.37700 53.35700 38.43450 number of atom coordinates read : 5497 total number of charged atoms : 5332 net assigned charge : -0.4859575 assigned positive charge : 828.4293 centred at (gu) : 90.06050 88.61474 89.13445 assigned negative charge : -828.9218 centred at (gu) : 89.88930 88.61096 89.03844 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8759 nv = 96 ne = 84 npr = 110036 no. pairs analyzed = 110036 no. exposed pairs = 6960 no. arc points = 48321 no. surface atoms = 2323 nbur = 3174 mkacc time = 0.1800000 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 = 1.708000 m= 274 mr = 4478 m= 0 mr = 5 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.3500000 number of dielectric boundary points 4550 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4750 ## 773 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 11796 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4602542E-10 1.4591149E-10 midg,1,midg; midg,igrid,midg -1.4215067E-11 3.4590334E-12 1,midg,midg; igrid,midg,midg -3.4222250E-10 3.3292274E-10 gauss-seidel spectral radius is 0.9796779 estimated iterations to convergence 58 setup time was (sec) 0.5400000 now iterating at: 08:56:42 rms-change max change #iterations 6.6169843E-02 9.468607 at 10iterations 3.7278675E-03 0.5147743 at 20iterations 3.9230386E-04 9.2244148E-02 at 30iterations 1.0215335E-04 2.4362564E-02 at 40iterations 3.0805328E-05 7.0285797E-03 at 50iterations finished qdiffx linear iterations at : 08:56:45 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 3.0805328E-05 7.0285797E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 08:56:45 3.533u 0.185s 0:03.98 93.2% 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 08:56:45 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5497 !!! WARNING: HIR 702 has a net charge of 0.5140 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: 1.502871 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): 3.845000 74.90900 ymin,ymax (A): 22.52600 84.18800 zmin,zma (A): 6.300000 70.56900 x,y,z range (A): 71.06400 61.66199 64.26900 scale (grids/A): 1.502871 object centre (A): 39.37700 53.35700 38.43450 number of atom coordinates read : 5497 total number of charged atoms : 5332 net assigned charge : -0.4859575 assigned positive charge : 828.4293 centred at (gu) : 90.17969 85.84241 87.40144 assigned negative charge : -828.9218 centred at (gu) : 89.66754 85.83270 87.11494 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 99084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48321 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 26868 mr = 67634 m= 2018 mr = 17185 m= 31 mr = 783 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2113 time to turn everything in is 0.4700000 number of dielectric boundary points 42400 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 750 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 39830 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) : 0.5009568 object centre at (A) : 39.37700 53.35700 38.43450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4719799E-03 1.0662714E-02 midg,1,midg; midg,igrid,midg -3.1553668E-03 -5.3252624E-03 1,midg,midg; igrid,midg,midg -9.5591294E-03 3.2430429E-02 gauss-seidel spectral radius is 0.9980989 estimated iterations to convergence 182 setup time was (sec) 0.6900000 now iterating at: 08:56:46 rms-change max change #iterations 3.936559 144.2905 at 10iterations 1.610761 52.71813 at 20iterations 0.6578348 20.71567 at 30iterations 0.2693932 9.641229 at 40iterations 0.1099932 3.382141 at 50iterations 4.4874795E-02 1.368031 at 60iterations 1.8424405E-02 0.5943069 at 70iterations 7.5666900E-03 0.2333937 at 80iterations 3.1192780E-03 8.8308334E-02 at 90iterations 1.2887558E-03 4.3342590E-02 at 100iterations 5.4156914E-04 1.6929626E-02 at 110iterations 2.3252907E-04 7.7190399E-03 at 120iterations finished qdiffx linear iterations at : 08:56:53 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 2.3252907E-04 7.7190399E-03 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 08:56:54 7.902u 0.197s 0:08.47 95.5% 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 08:56:54 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5497 !!! WARNING: HIR 702 has a net charge of 0.5140 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: 2.254306 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): 3.845000 74.90900 ymin,ymax (A): 22.52600 84.18800 zmin,zma (A): 6.300000 70.56900 x,y,z range (A): 71.06400 61.66199 64.26900 scale (grids/A): 2.254306 object centre (A): 39.37700 53.35700 38.43450 number of atom coordinates read : 5497 total number of charged atoms : 5332 net assigned charge : -0.4859575 assigned positive charge : 828.4293 centred at (gu) : 90.26923 83.76339 86.10173 assigned negative charge : -828.9218 centred at (gu) : 89.50099 83.74896 85.67231 start vw surface at 0.1300000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 231633 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48321 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 98318 mr = 166701 m= 22511 mr = 75391 m= 2695 mr = 15704 m= 127 mr = 1601 m= 0 mr = 44 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 6804 time to turn everything in is 1.130000 number of dielectric boundary points 95843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 42514 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) : 1.502871 object centre at (A) : 39.37700 53.35700 38.43450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2324377 0.1627890 midg,1,midg; midg,igrid,midg -6.5782942E-02 -8.3105899E-02 1,midg,midg; igrid,midg,midg -6.3404173E-02 0.5242104 gauss-seidel spectral radius is 0.9991780 estimated iterations to convergence 275 setup time was (sec) 1.380000 now iterating at: 08:56:56 rms-change max change #iterations 10.84616 336.8918 at 10iterations 6.279699 150.2493 at 20iterations 3.611862 83.35107 at 30iterations 2.063521 49.58241 at 40iterations 1.175959 23.08527 at 50iterations 0.6677976 13.25865 at 60iterations 0.3778344 8.728947 at 70iterations 0.2137602 3.845024 at 80iterations 0.1204485 2.474181 at 90iterations 6.7911439E-02 1.106770 at 100iterations 3.8279019E-02 0.7091675 at 110iterations 2.1472184E-02 0.3956566 at 120iterations 1.2076109E-02 0.2081146 at 130iterations 6.7939223E-03 0.1310139 at 140iterations 3.8128514E-03 6.6722393E-02 at 150iterations 2.1474103E-03 3.8829327E-02 at 160iterations 1.2063191E-03 2.3674011E-02 at 170iterations 6.8157766E-04 1.2193680E-02 at 180iterations finished qdiffx linear iterations at : 08:57:07 total time elapsed so far: 12.93000 # loops : 180 mean,max change (kT/e) : 6.8157766E-04 1.2193680E-02 energy calculations done at 12.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.06000 DelPhi exited at 08:57:07 13.065u 0.210s 0:13.54 98.0% 0+0k 0+0io 0pf+0w