Sun Oct 9 19:56:09 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 19:56:09 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5361 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 0.5186178 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): 3.242000 68.24300 ymin,ymax (A): -9.259000 53.25500 zmin,zma (A): -1.838000 66.80600 x,y,z range (A): 65.00101 62.51400 68.64400 scale (grids/A): 0.5186178 object centre (A): 35.74250 21.99800 32.48400 number of atom coordinates read : 5361 total number of charged atoms : 5211 net assigned charge : 3.740026 assigned positive charge : 824.5582 centred at (gu) : 88.08434 89.36141 88.65983 assigned negative charge : -820.8242 centred at (gu) : 87.99609 89.37044 88.58163 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 9113 nv = 96 ne = 84 npr = 109279 no. pairs analyzed = 109279 no. exposed pairs = 6092 no. arc points = 42067 no. surface atoms = 2085 nbur = 3276 mkacc time = 0.1900000 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 = 1.652000 m= 322 mr = 5104 m= 0 mr = 5 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4326 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4280 ## 577 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 12367 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4419723E-10 2.8839178E-10 midg,1,midg; midg,igrid,midg 1.4736432E-10 4.2910221E-11 1,midg,midg; igrid,midg,midg -4.7378912E-10 2.7353428E-10 gauss-seidel spectral radius is 0.9810154 estimated iterations to convergence 60 setup time was (sec) 0.5800000 now iterating at: 19:56:09 rms-change max change #iterations 8.5072048E-02 14.70620 at 10iterations 9.7954385E-03 1.482700 at 20iterations 3.5042481E-03 0.5884743 at 30iterations 1.4736394E-03 0.2407036 at 40iterations 6.2775519E-04 9.8930359E-02 at 50iterations finished qdiffx linear iterations at : 19:56:13 total time elapsed so far: 3.760000 # loops : 50 mean,max change (kT/e) : 6.2775519E-04 9.8930359E-02 energy calculations done at 3.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.910000 DelPhi exited at 19:56:13 3.910u 0.191s 0:04.42 92.7% 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 19:56:13 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5361 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.555853 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): 3.242000 68.24300 ymin,ymax (A): -9.259000 53.25500 zmin,zma (A): -1.838000 66.80600 x,y,z range (A): 65.00101 62.51400 68.64400 scale (grids/A): 1.555853 object centre (A): 35.74250 21.99800 32.48400 number of atom coordinates read : 5361 total number of charged atoms : 5211 net assigned charge : 3.740026 assigned positive charge : 824.5582 centred at (gu) : 84.25108 88.08241 85.97815 assigned negative charge : -820.8242 centred at (gu) : 83.98789 88.11080 85.74473 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 104466 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42067 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 31592 mr = 75558 m= 2946 mr = 21971 m= 74 mr = 1314 m= 0 mr = 14 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 40221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 541 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 39386 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) : 0.5186178 object centre at (A) : 35.74250 21.99800 32.48400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9253558E-02 2.7006280E-02 midg,1,midg; midg,igrid,midg 1.6039986E-02 5.8910130E-03 1,midg,midg; igrid,midg,midg -1.6026208E-02 9.4089139E-04 gauss-seidel spectral radius is 0.9982098 estimated iterations to convergence 188 setup time was (sec) 0.7500000 now iterating at: 19:56:14 rms-change max change #iterations 4.278930 189.6950 at 10iterations 1.797983 67.04589 at 20iterations 0.7535393 21.86353 at 30iterations 0.3187098 9.942150 at 40iterations 0.1344117 3.996305 at 50iterations 5.8050677E-02 1.675137 at 60iterations 2.5675870E-02 0.8327026 at 70iterations 1.2365291E-02 0.4351349 at 80iterations 6.8020737E-03 0.2430267 at 90iterations 4.2463052E-03 0.1422157 at 100iterations 2.9121079E-03 0.1001091 at 110iterations 2.0728752E-03 7.0476532E-02 at 120iterations finished qdiffx linear iterations at : 19:56:22 total time elapsed so far: 8.180000 # loops : 120 mean,max change (kT/e) : 2.0728752E-03 7.0476532E-02 energy calculations done at 8.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.300000 DelPhi exited at 19:56:23 8.304u 0.857s 0:09.63 95.0% 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 Sun Oct 9 2011 at 19:56:23 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5361 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 2.333780 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): 3.242000 68.24300 ymin,ymax (A): -9.259000 53.25500 zmin,zma (A): -1.838000 66.80600 x,y,z range (A): 65.00101 62.51400 68.64400 scale (grids/A): 2.333780 object centre (A): 35.74250 21.99800 32.48400 number of atom coordinates read : 5361 total number of charged atoms : 5211 net assigned charge : 3.740026 assigned positive charge : 824.5582 centred at (gu) : 81.37614 87.12305 83.96715 assigned negative charge : -820.8242 centred at (gu) : 80.98180 87.16632 83.61687 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 243973 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42067 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 113018 mr = 184802 m= 29933 mr = 90925 m= 4358 mr = 22306 m= 274 mr = 2680 m= 4 mr = 130 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 90717 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 41573 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) : 1.555853 object centre at (A) : 35.74250 21.99800 32.48400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4794948 0.8682927 midg,1,midg; midg,igrid,midg 0.2794986 4.7239289E-02 1,midg,midg; igrid,midg,midg -0.3677494 2.4206258E-04 gauss-seidel spectral radius is 0.9991895 estimated iterations to convergence 277 setup time was (sec) 1.510000 now iterating at: 19:56:25 rms-change max change #iterations 11.20091 305.8924 at 10iterations 6.417294 143.5768 at 20iterations 3.647043 73.47066 at 30iterations 2.065755 42.32314 at 40iterations 1.168883 20.93203 at 50iterations 0.6599389 12.61131 at 60iterations 0.3708660 6.755071 at 70iterations 0.2094053 3.864243 at 80iterations 0.1178480 2.539774 at 90iterations 6.6634074E-02 1.227077 at 100iterations 3.7865315E-02 0.6981773 at 110iterations 2.1844391E-02 0.4331131 at 120iterations 1.2885456E-02 0.2415047 at 130iterations 7.9078004E-03 0.1474915 at 140iterations 5.1436117E-03 0.1097488 at 150iterations 3.5804233E-03 7.3822021E-02 at 160iterations 2.6477948E-03 5.7983398E-02 at 170iterations 2.0412009E-03 4.3884277E-02 at 180iterations finished qdiffx linear iterations at : 19:56:36 total time elapsed so far: 13.33000 # loops : 180 mean,max change (kT/e) : 2.0412009E-03 4.3884277E-02 energy calculations done at 13.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.48000 DelPhi exited at 19:56:37 13.480u 0.232s 0:14.17 96.7% 0+0k 0+0io 0pf+0w