Sat Oct 8 17:10:05 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 17:10:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3215 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5509045 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): 37.84300 93.63300 ymin,ymax (A): 16.51600 81.13700 zmin,zma (A): -22.82700 26.07500 x,y,z range (A): 55.78999 64.62100 48.90200 scale (grids/A): 0.5509045 object centre (A): 65.73800 48.82650 1.624000 number of atom coordinates read : 3215 total number of charged atoms : 3070 net assigned charge : -5.499977 assigned positive charge : 477.7759 centred at (gu) : 90.06745 90.68152 89.92311 assigned negative charge : -483.2771 centred at (gu) : 90.02969 90.66211 89.91350 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6423 nv = 96 ne = 84 npr = 65056 no. pairs analyzed = 65056 no. exposed pairs = 3995 no. arc points = 27555 no. surface atoms = 1352 nbur = 1863 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 = 1.568000 m= 274 mr = 3457 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3228 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2796 ## 358 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8333 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.0890936E-10 -3.2687331E-10 midg,1,midg; midg,igrid,midg -4.9645932E-10 -2.9047162E-10 1,midg,midg; igrid,midg,midg -7.3312117E-10 -9.1246385E-11 gauss-seidel spectral radius is 0.9830269 estimated iterations to convergence 63 setup time was (sec) 0.6800000 now iterating at: 17:10:06 rms-change max change #iterations 8.0961190E-02 12.55676 at 10iterations 5.5468795E-03 0.9303684 at 20iterations 3.9715966E-04 7.6131821E-02 at 30iterations 3.7485723E-05 7.1220398E-03 at 40iterations 5.9432409E-06 1.2192726E-03 at 50iterations finished qdiffx linear iterations at : 17:10:09 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 5.9432409E-06 1.2192726E-03 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.260000 DelPhi exited at 17:10:10 4.260u 0.295s 0:04.88 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 Sat Oct 8 2011 at 17:10:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3215 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: 1.652713 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): 37.84300 93.63300 ymin,ymax (A): 16.51600 81.13700 zmin,zma (A): -22.82700 26.07500 x,y,z range (A): 55.78999 64.62100 48.90200 scale (grids/A): 1.652713 object centre (A): 65.73800 48.82650 1.624000 number of atom coordinates read : 3215 total number of charged atoms : 3070 net assigned charge : -5.499977 assigned positive charge : 477.7759 centred at (gu) : 90.20171 92.04395 89.76852 assigned negative charge : -483.2771 centred at (gu) : 90.08880 91.98597 89.74050 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 70945 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27555 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23490 mr = 49464 m= 2750 mr = 16658 m= 116 mr = 1457 m= 0 mr = 9 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 233 time to turn everything in is 0.6300000 number of dielectric boundary points 29713 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 320 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 23553 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) : 0.5509045 object centre at (A) : 65.73800 48.82650 1.624000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4958935E-03 -4.3034959E-03 midg,1,midg; midg,igrid,midg -8.7826233E-03 1.7599801E-02 1,midg,midg; igrid,midg,midg -1.5425186E-02 -2.8165965E-03 gauss-seidel spectral radius is 0.9982554 estimated iterations to convergence 190 setup time was (sec) 0.9100000 now iterating at: 17:10:11 rms-change max change #iterations 3.543046 162.9866 at 10iterations 1.493955 59.79081 at 20iterations 0.6375383 21.12759 at 30iterations 0.2707021 8.965355 at 40iterations 0.1147844 4.535528 at 50iterations 4.8810344E-02 1.820220 at 60iterations 2.0763818E-02 0.7198334 at 70iterations 8.8056503E-03 0.3004379 at 80iterations 3.7575259E-03 0.1486268 at 90iterations 1.5994181E-03 6.1382294E-02 at 100iterations 6.8160030E-04 2.2342682E-02 at 110iterations 2.9410326E-04 1.0044098E-02 at 120iterations finished qdiffx linear iterations at : 17:10:20 total time elapsed so far: 9.500000 # loops : 120 mean,max change (kT/e) : 2.9410326E-04 1.0044098E-02 energy calculations done at 9.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.670000 DelPhi exited at 17:10:20 9.676u 0.386s 0:10.36 97.0% 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 Sat Oct 8 2011 at 17:10:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3215 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: 2.479070 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): 37.84300 93.63300 ymin,ymax (A): 16.51600 81.13700 zmin,zma (A): -22.82700 26.07500 x,y,z range (A): 55.78999 64.62100 48.90200 scale (grids/A): 2.479070 object centre (A): 65.73800 48.82650 1.624000 number of atom coordinates read : 3215 total number of charged atoms : 3070 net assigned charge : -5.499977 assigned positive charge : 477.7759 centred at (gu) : 90.30240 93.06554 89.65239 assigned negative charge : -483.2771 centred at (gu) : 90.13307 92.97864 89.61041 start vw surface at 0.1700000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 164416 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27555 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 79824 mr = 120111 m= 24501 mr = 64316 m= 4522 mr = 18913 m= 373 mr = 3077 m= 7 mr = 177 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 839 time to turn everything in is 1.600000 number of dielectric boundary points 67049 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 24543 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) : 1.652713 object centre at (A) : 65.73800 48.82650 1.624000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.6271599E-02 -3.6533989E-02 midg,1,midg; midg,igrid,midg -0.2046969 0.5537774 1,midg,midg; igrid,midg,midg -0.2276836 -1.8571278E-02 gauss-seidel spectral radius is 0.9991642 estimated iterations to convergence 273 setup time was (sec) 1.930000 now iterating at: 17:10:23 rms-change max change #iterations 9.063197 287.1253 at 10iterations 5.120918 109.8891 at 20iterations 2.870495 59.59996 at 30iterations 1.608998 34.97634 at 40iterations 0.8989841 18.55801 at 50iterations 0.4989448 9.893086 at 60iterations 0.2787500 5.638910 at 70iterations 0.1546392 3.077827 at 80iterations 8.5904814E-02 1.657001 at 90iterations 4.7730677E-02 0.9457436 at 100iterations 2.6527649E-02 0.5137587 at 110iterations 1.4678858E-02 0.2817781 at 120iterations 8.1775505E-03 0.1643538 at 130iterations 4.5315940E-03 8.5493878E-02 at 140iterations 2.5139735E-03 4.7813416E-02 at 150iterations 1.3979333E-03 2.8202057E-02 at 160iterations 7.7671977E-04 1.5491486E-02 at 170iterations 4.3200442E-04 8.2321167E-03 at 180iterations finished qdiffx linear iterations at : 17:10:37 total time elapsed so far: 16.15000 # loops : 180 mean,max change (kT/e) : 4.3200442E-04 8.2321167E-03 energy calculations done at 16.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.33000 DelPhi exited at 17:10:37 16.334u 0.358s 0:16.95 98.4% 0+0k 0+0io 0pf+0w