Tue Oct 11 03:19:16 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 Tue Oct 11 2011 at 03:19:16 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 = 3158 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5368479 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): -6.5000057E-02 46.31700 ymin,ymax (A): 70.95000 137.2630 zmin,zma (A): 102.3240 161.6830 x,y,z range (A): 46.38200 66.31300 59.35900 scale (grids/A): 0.5368479 object centre (A): 23.12600 104.1065 132.0035 number of atom coordinates read : 3158 total number of charged atoms : 3019 net assigned charge : -5.999976 assigned positive charge : 470.0839 centred at (gu) : 90.38564 92.85207 91.53478 assigned negative charge : -476.0849 centred at (gu) : 90.33984 92.88237 91.53426 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5720 nv = 96 ne = 84 npr = 65729 no. pairs analyzed = 65729 no. exposed pairs = 3821 no. arc points = 26204 no. surface atoms = 1298 nbur = 1860 mkacc time = 0.1800000 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 = 1.596000 m= 204 mr = 3051 m= 0 mr = 11 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 2862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2716 ## 409 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7684 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7595719E-10 -3.6429004E-10 midg,1,midg; midg,igrid,midg -5.4299145E-11 -8.2857288E-10 1,midg,midg; igrid,midg,midg -4.3675724E-10 -2.8203426E-11 gauss-seidel spectral radius is 0.9821239 estimated iterations to convergence 62 setup time was (sec) 0.6500000 now iterating at: 03:19:46 rms-change max change #iterations 7.1375102E-02 10.40457 at 10iterations 4.7465251E-03 0.8182380 at 20iterations 3.6701965E-04 7.1987152E-02 at 30iterations 5.3102300E-05 1.0622382E-02 at 40iterations 1.1208884E-05 2.3967028E-03 at 50iterations finished qdiffx linear iterations at : 03:19:51 total time elapsed so far: 4.920000 # loops : 50 mean,max change (kT/e) : 1.1208884E-05 2.3967028E-03 energy calculations done at 4.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.090000 DelPhi exited at 03:19:51 5.092u 0.527s 0:34.84 16.1% 0+0k 0+0io 4pf+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 03:19:51 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 = 3158 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: 1.610544 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): -6.5000057E-02 46.31700 ymin,ymax (A): 70.95000 137.2630 zmin,zma (A): 102.3240 161.6830 x,y,z range (A): 46.38200 66.31300 59.35900 scale (grids/A): 1.610544 object centre (A): 23.12600 104.1065 132.0035 number of atom coordinates read : 3158 total number of charged atoms : 3019 net assigned charge : -5.999976 assigned positive charge : 470.0839 centred at (gu) : 91.15609 98.55531 94.60342 assigned negative charge : -476.0849 centred at (gu) : 91.01925 98.64658 94.60228 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 63725 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26204 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 19168 mr = 43772 m= 1895 mr = 13331 m= 36 mr = 925 m= 0 mr = 2 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 339 time to turn everything in is 0.5700000 number of dielectric boundary points 26794 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 374 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 23006 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) : 0.5368479 object centre at (A) : 23.12600 104.1065 132.0035 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0067964E-03 3.0323293E-03 midg,1,midg; midg,igrid,midg 2.2587704E-02 -6.7143040E-03 1,midg,midg; igrid,midg,midg -9.4391536E-03 -3.7318591E-03 gauss-seidel spectral radius is 0.9981335 estimated iterations to convergence 184 setup time was (sec) 0.8900000 now iterating at: 03:19:53 rms-change max change #iterations 3.305064 143.5441 at 10iterations 1.357004 50.95011 at 20iterations 0.5604715 19.77922 at 30iterations 0.2314782 8.286394 at 40iterations 9.5154114E-02 3.735136 at 50iterations 3.9380051E-02 1.473170 at 60iterations 1.6262783E-02 0.5995896 at 70iterations 6.7113764E-03 0.2433414 at 80iterations 2.7971566E-03 0.1118612 at 90iterations 1.1645471E-03 4.6413422E-02 at 100iterations 4.9304334E-04 2.0603180E-02 at 110iterations 2.1456905E-04 9.0546608E-03 at 120iterations finished qdiffx linear iterations at : 03:20:04 total time elapsed so far: 11.94000 # loops : 120 mean,max change (kT/e) : 2.1456905E-04 9.0546608E-03 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.11000 DelPhi exited at 03:20:04 12.119u 0.516s 0:12.95 97.4% 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 03:20:04 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 = 3158 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.415816 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): -6.5000057E-02 46.31700 ymin,ymax (A): 70.95000 137.2630 zmin,zma (A): 102.3240 161.6830 x,y,z range (A): 46.38200 66.31300 59.35900 scale (grids/A): 2.415816 object centre (A): 23.12600 104.1065 132.0035 number of atom coordinates read : 3158 total number of charged atoms : 3019 net assigned charge : -5.999976 assigned positive charge : 470.0839 centred at (gu) : 91.73401 102.8327 96.90501 assigned negative charge : -476.0849 centred at (gu) : 91.52868 102.9696 96.90330 start vw surface at 0.1300000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 148368 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26204 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 67355 mr = 107247 m= 18294 mr = 53510 m= 2924 mr = 13818 m= 177 mr = 1893 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 1065 time to turn everything in is 1.330000 number of dielectric boundary points 60593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 24114 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) : 1.610544 object centre at (A) : 23.12600 104.1065 132.0035 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3945466E-02 0.1413302 midg,1,midg; midg,igrid,midg 0.4081999 -0.2889423 1,midg,midg; igrid,midg,midg -0.1541148 -4.7144342E-02 gauss-seidel spectral radius is 0.9991205 estimated iterations to convergence 266 setup time was (sec) 1.670000 now iterating at: 03:20:06 rms-change max change #iterations 8.616828 277.9651 at 10iterations 4.808791 123.4452 at 20iterations 2.668202 61.09081 at 30iterations 1.475207 34.45563 at 40iterations 0.8115699 18.66192 at 50iterations 0.4468592 9.646343 at 60iterations 0.2457277 5.063273 at 70iterations 0.1345578 2.837280 at 80iterations 7.3773302E-02 1.813556 at 90iterations 4.0353972E-02 0.9254687 at 100iterations 2.2060685E-02 0.4499550 at 110iterations 1.2072559E-02 0.2504406 at 120iterations 6.6155707E-03 0.1337686 at 130iterations 3.6082356E-03 7.1605682E-02 at 140iterations 1.9718062E-03 4.2128563E-02 at 150iterations 1.0769216E-03 2.4696350E-02 at 160iterations 5.8861973E-04 1.1971474E-02 at 170iterations 3.2178633E-04 6.8407059E-03 at 180iterations finished qdiffx linear iterations at : 03:20:24 total time elapsed so far: 19.04000 # loops : 180 mean,max change (kT/e) : 3.2178633E-04 6.8407059E-03 energy calculations done at 19.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.21000 DelPhi exited at 03:20:24 19.216u 0.554s 0:20.02 98.7% 0+0k 0+0io 0pf+0w