Tue Oct 11 04:25:57 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 Tue Oct 11 2011 at 04:25:57 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2697 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6583692 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): -11.20500 37.08800 ymin,ymax (A): -26.30500 22.31600 zmin,zma (A): -8.231999 45.84100 x,y,z range (A): 48.29300 48.62100 54.07300 scale (grids/A): 0.6583692 object centre (A): 12.94150 -1.994500 18.80450 number of atom coordinates read : 2697 total number of charged atoms : 2549 net assigned charge : 3.500022 assigned positive charge : 410.4977 centred at (gu) : 90.08892 90.35114 91.23566 assigned negative charge : -406.9984 centred at (gu) : 89.84462 90.17637 91.26920 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7828 nv = 96 ne = 84 npr = 55323 no. pairs analyzed = 55323 no. exposed pairs = 3280 no. arc points = 22843 no. surface atoms = 1110 nbur = 1587 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 436 mr = 4472 m= 5 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.2100000 number of dielectric boundary points 3757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2165 ## 183 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9229 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1765334E-08 2.2058910E-09 midg,1,midg; midg,igrid,midg -2.4909637E-08 4.5874664E-08 1,midg,midg; igrid,midg,midg -4.0541639E-08 5.6874295E-08 gauss-seidel spectral radius is 0.9880487 estimated iterations to convergence 75 setup time was (sec) 0.4100000 now iterating at: 04:25:58 rms-change max change #iterations 0.1723301 28.34317 at 10iterations 1.8200373E-02 2.664970 at 20iterations 1.9531618E-03 0.2506733 at 30iterations 2.1928843E-04 3.0970097E-02 at 40iterations 2.7425434E-05 3.7612915E-03 at 50iterations finished qdiffx linear iterations at : 04:26:01 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 2.7425434E-05 3.7612915E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 04:26:01 3.432u 0.172s 0:04.10 87.8% 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 Tue Oct 11 2011 at 04:26:01 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2697 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.975108 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): -11.20500 37.08800 ymin,ymax (A): -26.30500 22.31600 zmin,zma (A): -8.231999 45.84100 x,y,z range (A): 48.29300 48.62100 54.07300 scale (grids/A): 1.975108 object centre (A): 12.94150 -1.994500 18.80450 number of atom coordinates read : 2697 total number of charged atoms : 2549 net assigned charge : 3.500022 assigned positive charge : 410.4977 centred at (gu) : 90.26654 91.05309 93.70641 assigned negative charge : -406.9984 centred at (gu) : 89.53353 90.52879 93.80708 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 84623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22843 grid for indexing accessible points = 1.400000 m= 31067 mr = 59982 m= 5003 mr = 23191 m= 275 mr = 3005 m= 3 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 211 time to turn everything in is 0.4200000 number of dielectric boundary points 34702 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 20120 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) : 0.6583692 object centre at (A) : 12.94150 -1.994500 18.80450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9220959E-02 -1.2430006E-02 midg,1,midg; midg,igrid,midg -1.4632175E-02 3.9771132E-02 1,midg,midg; igrid,midg,midg -1.3166741E-02 6.9856092E-02 gauss-seidel spectral radius is 0.9987372 estimated iterations to convergence 223 setup time was (sec) 0.6300000 now iterating at: 04:26:02 rms-change max change #iterations 4.682105 181.4964 at 10iterations 2.262069 73.29610 at 20iterations 1.092978 32.98377 at 30iterations 0.5248144 15.48448 at 40iterations 0.2552273 8.617537 at 50iterations 0.1232155 3.787596 at 60iterations 5.9075560E-02 1.763806 at 70iterations 2.8592238E-02 0.8004885 at 80iterations 1.3799991E-02 0.4275293 at 90iterations 6.6732466E-03 0.1868515 at 100iterations 3.2197649E-03 9.9851608E-02 at 110iterations 1.5533022E-03 4.5072556E-02 at 120iterations finished qdiffx linear iterations at : 04:26:09 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 1.5533022E-03 4.5072556E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 04:26:10 7.925u 0.203s 0:08.54 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 Tue Oct 11 2011 at 04:26:10 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2697 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.962662 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): -11.20500 37.08800 ymin,ymax (A): -26.30500 22.31600 zmin,zma (A): -8.231999 45.84100 x,y,z range (A): 48.29300 48.62100 54.07300 scale (grids/A): 2.962662 object centre (A): 12.94150 -1.994500 18.80450 number of atom coordinates read : 2697 total number of charged atoms : 2549 net assigned charge : 3.500022 assigned positive charge : 410.4977 centred at (gu) : 90.39944 91.57941 95.55946 assigned negative charge : -406.9984 centred at (gu) : 89.30023 90.79307 95.71066 start vw surface at 0.1000000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 195379 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22843 grid for indexing accessible points = 1.400000 m= 100941 mr = 144694 m= 36649 mr = 83273 m= 8888 mr = 29499 m= 1333 mr = 6690 m= 69 mr = 825 m= 0 mr = 18 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 703 time to turn everything in is 1.080000 number of dielectric boundary points 78260 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 20392 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) : 1.975108 object centre at (A) : 12.94150 -1.994500 18.80450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5964780 0.1215672 midg,1,midg; midg,igrid,midg -0.1562766 0.4695981 1,midg,midg; igrid,midg,midg -8.0428272E-02 0.5825235 gauss-seidel spectral radius is 0.9992813 estimated iterations to convergence 294 setup time was (sec) 1.320000 now iterating at: 04:26:12 rms-change max change #iterations 10.77573 399.2318 at 10iterations 6.312418 139.3285 at 20iterations 3.692115 66.68152 at 30iterations 2.152671 38.14906 at 40iterations 1.257765 25.01616 at 50iterations 0.7345121 13.87005 at 60iterations 0.4268994 7.366075 at 70iterations 0.2484051 4.269630 at 80iterations 0.1441230 2.470306 at 90iterations 8.3762057E-02 1.415131 at 100iterations 4.8783913E-02 0.9081802 at 110iterations 2.8350910E-02 0.4886703 at 120iterations 1.6453706E-02 0.2793140 at 130iterations 9.5543507E-03 0.1765312 at 140iterations 5.5551250E-03 0.1001015 at 150iterations 3.2352649E-03 5.9429169E-02 at 160iterations 1.8851320E-03 3.2781601E-02 at 170iterations 1.1110863E-03 1.9098282E-02 at 180iterations finished qdiffx linear iterations at : 04:26:23 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 1.1110863E-03 1.9098282E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 04:26:24 12.942u 0.225s 0:13.63 96.5% 0+0k 0+0io 0pf+0w