Sun Oct 9 19:55:40 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 19:55:40 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 = 5391 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4994459 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): 3.290000 68.24000 ymin,ymax (A): -8.681000 53.56600 zmin,zma (A): -2.390000 68.88900 x,y,z range (A): 64.95000 62.24700 71.27900 scale (grids/A): 0.4994459 object centre (A): 35.76500 22.44250 33.24950 number of atom coordinates read : 5391 total number of charged atoms : 5235 net assigned charge : 4.754030 assigned positive charge : 833.7422 centred at (gu) : 88.36327 89.26810 88.75260 assigned negative charge : -828.9940 centred at (gu) : 88.30367 89.29770 88.68558 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8583 nv = 96 ne = 84 npr = 108630 no. pairs analyzed = 108630 no. exposed pairs = 6262 no. arc points = 42727 no. surface atoms = 2131 nbur = 3260 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 = 1.736000 m= 298 mr = 4763 m= 0 mr = 5 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 4113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4201 ## 604 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 11511 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1448144E-10 1.1858484E-10 midg,1,midg; midg,igrid,midg 1.1914522E-10 -8.6692702E-12 1,midg,midg; igrid,midg,midg -1.0608610E-10 9.8332807E-11 gauss-seidel spectral radius is 0.9795398 estimated iterations to convergence 58 setup time was (sec) 0.7500000 now iterating at: 19:55:41 rms-change max change #iterations 7.2813272E-02 11.19483 at 10iterations 9.4321314E-03 1.564140 at 20iterations 3.8259281E-03 0.7144012 at 30iterations 1.7281756E-03 0.3199387 at 40iterations 7.9105020E-04 0.1433487 at 50iterations finished qdiffx linear iterations at : 19:55:43 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 7.9105020E-04 0.1433487 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 19:55:44 3.566u 0.144s 0:03.99 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 19:55:44 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 = 5391 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.498338 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): 3.290000 68.24000 ymin,ymax (A): -8.681000 53.56600 zmin,zma (A): -2.390000 68.88900 x,y,z range (A): 64.95000 62.24700 71.27900 scale (grids/A): 1.498338 object centre (A): 35.76500 22.44250 33.24950 number of atom coordinates read : 5391 total number of charged atoms : 5235 net assigned charge : 4.754030 assigned positive charge : 833.7422 centred at (gu) : 85.08858 87.80325 86.25571 assigned negative charge : -828.9940 centred at (gu) : 84.91080 87.89278 86.05669 start vw surface at 0.2300000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 98438 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42727 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 30045 mr = 70874 m= 2496 mr = 20786 m= 39 mr = 1039 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 38319 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 569 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 39011 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) : 0.4994459 object centre at (A) : 35.76500 22.44250 33.24950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0403344E-02 1.4431650E-02 midg,1,midg; midg,igrid,midg 1.1033035E-02 4.2824456E-03 1,midg,midg; igrid,midg,midg -8.5920421E-03 3.7320194E-04 gauss-seidel spectral radius is 0.9980574 estimated iterations to convergence 180 setup time was (sec) 1.020000 now iterating at: 19:55:45 rms-change max change #iterations 3.938473 154.4856 at 10iterations 1.598005 64.22306 at 20iterations 0.6472046 21.15235 at 30iterations 0.2635526 8.434933 at 40iterations 0.1077776 3.503021 at 50iterations 4.5065429E-02 1.339218 at 60iterations 1.9902907E-02 0.6253815 at 70iterations 9.9984230E-03 0.3298836 at 80iterations 5.9887511E-03 0.2229309 at 90iterations 4.0447749E-03 0.1416550 at 100iterations 2.9264218E-03 9.8854065E-02 at 110iterations 2.1578323E-03 7.2238922E-02 at 120iterations finished qdiffx linear iterations at : 19:55:51 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 2.1578323E-03 7.2238922E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 19:55:52 7.682u 0.159s 0:08.13 96.3% 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 Sun Oct 9 2011 at 19:55:52 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 = 5391 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.247506 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): 3.290000 68.24000 ymin,ymax (A): -8.681000 53.56600 zmin,zma (A): -2.390000 68.88900 x,y,z range (A): 64.95000 62.24700 71.27900 scale (grids/A): 2.247506 object centre (A): 35.76500 22.44250 33.24950 number of atom coordinates read : 5391 total number of charged atoms : 5235 net assigned charge : 4.754030 assigned positive charge : 833.7422 centred at (gu) : 82.63246 86.70444 84.38320 assigned negative charge : -828.9940 centred at (gu) : 82.36616 86.83910 84.08500 start vw surface at 0.2200000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 229673 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42727 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 107818 mr = 173298 m= 27866 mr = 86497 m= 3551 mr = 20576 m= 157 mr = 2077 m= 0 mr = 61 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.730000 number of dielectric boundary points 86556 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 41679 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) : 1.498338 object centre at (A) : 35.76500 22.44250 33.24950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2993440 0.5647974 midg,1,midg; midg,igrid,midg 0.2076108 5.1305365E-02 1,midg,midg; igrid,midg,midg -0.2447211 -3.7989046E-03 gauss-seidel spectral radius is 0.9991458 estimated iterations to convergence 270 setup time was (sec) 2.050000 now iterating at: 19:55:54 rms-change max change #iterations 10.65184 284.7222 at 10iterations 6.033582 132.0612 at 20iterations 3.382386 72.35419 at 30iterations 1.891463 36.02558 at 40iterations 1.053477 20.65583 at 50iterations 0.5868708 11.27975 at 60iterations 0.3250625 7.201416 at 70iterations 0.1806741 3.171959 at 80iterations 0.1003203 1.963587 at 90iterations 5.5797830E-02 1.010468 at 100iterations 3.1314470E-02 0.5646815 at 110iterations 1.7828805E-02 0.3279800 at 120iterations 1.0458054E-02 0.2319717 at 130iterations 6.4402274E-03 0.1422729 at 140iterations 4.2523481E-03 9.3326569E-02 at 150iterations 3.0347046E-03 6.3888550E-02 at 160iterations 2.3050616E-03 4.7370911E-02 at 170iterations 1.8158848E-03 3.6918640E-02 at 180iterations finished qdiffx linear iterations at : 19:56:05 total time elapsed so far: 12.96000 # loops : 180 mean,max change (kT/e) : 1.8158848E-03 3.6918640E-02 energy calculations done at 12.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 19:56:06 13.159u 0.177s 0:13.69 97.2% 0+0k 0+0io 0pf+0w