Mon Oct 10 10:24:27 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 Mon Oct 10 2011 at 10:24:27 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 = 2846 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: 0.5653127 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): 111.7920 174.7660 ymin,ymax (A): -41.70100 10.61200 zmin,zma (A): 48.10100 104.7300 x,y,z range (A): 62.97399 52.31300 56.62900 scale (grids/A): 0.5653127 object centre (A): 143.2790 -15.54450 76.41550 number of atom coordinates read : 2846 total number of charged atoms : 2698 net assigned charge : 6.000015 assigned positive charge : 418.6080 centred at (gu) : 89.25607 88.38778 88.82496 assigned negative charge : -412.6084 centred at (gu) : 89.39436 88.49763 88.69142 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5939 nv = 96 ne = 84 npr = 55844 no. pairs analyzed = 55844 no. exposed pairs = 4355 no. arc points = 31537 no. surface atoms = 1437 nbur = 1409 mkacc time = 0.1400000 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 = 1.512000 m= 312 mr = 2448 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3790 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3096 ## 350 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7642 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2378583E-09 1.7986069E-09 midg,1,midg; midg,igrid,midg 3.0964196E-09 -4.0650819E-10 1,midg,midg; igrid,midg,midg 2.9156777E-09 -8.0950030E-10 gauss-seidel spectral radius is 0.9838628 estimated iterations to convergence 65 setup time was (sec) 0.5900000 now iterating at: 10:24:28 rms-change max change #iterations 8.5644022E-02 15.66509 at 10iterations 6.1055315E-03 1.081209 at 20iterations 4.3568594E-04 6.7855835E-02 at 30iterations 3.2168093E-05 4.8532486E-03 at 40iterations 2.3826731E-06 3.9672852E-04 at 50iterations finished qdiffx linear iterations at : 10:24:31 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 2.3826731E-06 3.9672852E-04 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 10:24:31 3.630u 0.214s 0:04.25 90.3% 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 Mon Oct 10 2011 at 10:24:31 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 = 2846 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: 1.695938 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): 111.7920 174.7660 ymin,ymax (A): -41.70100 10.61200 zmin,zma (A): 48.10100 104.7300 x,y,z range (A): 62.97399 52.31300 56.62900 scale (grids/A): 1.695938 object centre (A): 143.2790 -15.54450 76.41550 number of atom coordinates read : 2846 total number of charged atoms : 2698 net assigned charge : 6.000015 assigned positive charge : 418.6080 centred at (gu) : 87.76775 85.16299 86.47462 assigned negative charge : -412.6084 centred at (gu) : 88.18290 85.49276 86.07396 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 62575 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31537 grid for indexing accessible points = 1.400000 m= 19692 mr = 36472 m= 2865 mr = 12368 m= 115 mr = 1382 m= 0 mr = 11 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 35014 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 265 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 20860 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) : 0.5653127 object centre at (A) : 143.2790 -15.54450 76.41550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0093581E-02 1.9672045E-02 midg,1,midg; midg,igrid,midg 1.7207718E-02 1.6069863E-03 1,midg,midg; igrid,midg,midg 3.0776067E-02 -2.6675353E-03 gauss-seidel spectral radius is 0.9983323 estimated iterations to convergence 194 setup time was (sec) 0.8200000 now iterating at: 10:24:32 rms-change max change #iterations 3.483842 153.0862 at 10iterations 1.503086 55.58408 at 20iterations 0.6490772 26.44789 at 30iterations 0.2806118 12.00947 at 40iterations 0.1209159 5.019154 at 50iterations 5.2127905E-02 1.846153 at 60iterations 2.2503020E-02 0.8078270 at 70iterations 9.6975435E-03 0.3538094 at 80iterations 4.1997903E-03 0.1549358 at 90iterations 1.8067592E-03 6.5297484E-02 at 100iterations 7.8499160E-04 3.1852782E-02 at 110iterations 3.3886731E-04 1.2713194E-02 at 120iterations finished qdiffx linear iterations at : 10:24:41 total time elapsed so far: 8.940000 # loops : 120 mean,max change (kT/e) : 3.3886731E-04 1.2713194E-02 energy calculations done at 8.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.140000 DelPhi exited at 10:24:41 9.141u 0.288s 0:09.78 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 Mon Oct 10 2011 at 10:24:41 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2846 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: 2.543907 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): 111.7920 174.7660 ymin,ymax (A): -41.70100 10.61200 zmin,zma (A): 48.10100 104.7300 x,y,z range (A): 62.97399 52.31300 56.62900 scale (grids/A): 2.543907 object centre (A): 143.2790 -15.54450 76.41550 number of atom coordinates read : 2846 total number of charged atoms : 2698 net assigned charge : 6.000015 assigned positive charge : 418.6080 centred at (gu) : 86.65149 82.74429 84.71191 assigned negative charge : -412.6084 centred at (gu) : 87.27432 83.23903 84.11089 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 144840 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31537 grid for indexing accessible points = 1.400000 m= 63240 mr = 90900 m= 21625 mr = 46142 m= 4666 mr = 15577 m= 454 mr = 2988 m= 18 mr = 196 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 79040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 21569 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) : 1.695938 object centre at (A) : 143.2790 -15.54450 76.41550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1454719 0.2618532 midg,1,midg; midg,igrid,midg 0.2489807 5.5722162E-02 1,midg,midg; igrid,midg,midg 0.2214951 -4.5382369E-02 gauss-seidel spectral radius is 0.9992014 estimated iterations to convergence 279 setup time was (sec) 1.660000 now iterating at: 10:24:43 rms-change max change #iterations 9.027432 340.3393 at 10iterations 5.293424 140.5252 at 20iterations 3.063321 83.54604 at 30iterations 1.759576 49.23856 at 40iterations 1.006804 26.97517 at 50iterations 0.5733106 15.70597 at 60iterations 0.3266176 10.07133 at 70iterations 0.1850333 5.730991 at 80iterations 0.1050251 2.538894 at 90iterations 5.9337158E-02 1.632837 at 100iterations 3.3456113E-02 0.8161459 at 110iterations 1.8928576E-02 0.4240851 at 120iterations 1.0658495E-02 0.2936630 at 130iterations 6.0117142E-03 0.1665659 at 140iterations 3.3881634E-03 7.5963974E-02 at 150iterations 1.9083648E-03 4.0142298E-02 at 160iterations 1.0766586E-03 2.6817605E-02 at 170iterations 6.0717453E-04 1.3081074E-02 at 180iterations finished qdiffx linear iterations at : 10:24:55 total time elapsed so far: 13.35000 # loops : 180 mean,max change (kT/e) : 6.0717453E-04 1.3081074E-02 energy calculations done at 13.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.57000 DelPhi exited at 10:24:56 13.569u 0.297s 0:14.24 97.2% 0+0k 0+0io 0pf+0w