Mon Oct 10 14:39:39 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 14:39:39 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2377 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6577610 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): -22.75500 31.36800 ymin,ymax (A): 12.15600 58.13100 zmin,zma (A): 28.07900 78.25800 x,y,z range (A): 54.12300 45.97500 50.17900 scale (grids/A): 0.6577610 object centre (A): 4.306500 35.14350 53.16850 number of atom coordinates read : 2377 total number of charged atoms : 2244 net assigned charge : -2.499994 assigned positive charge : 360.4772 centred at (gu) : 89.63722 90.74220 90.28573 assigned negative charge : -362.9778 centred at (gu) : 89.85188 90.71537 90.38515 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6904 nv = 96 ne = 84 npr = 49259 no. pairs analyzed = 49259 no. exposed pairs = 2939 no. arc points = 20683 no. surface atoms = 1006 nbur = 1371 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 405 mr = 3840 m= 0 mr = 64 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.1900000 number of dielectric boundary points 3405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2009 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8169 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0449125E-08 -2.5076533E-08 midg,1,midg; midg,igrid,midg -9.2371497E-09 -1.5650896E-09 1,midg,midg; igrid,midg,midg 3.3079736E-08 -4.1150031E-08 gauss-seidel spectral radius is 0.9880028 estimated iterations to convergence 75 setup time was (sec) 0.3700000 now iterating at: 14:39:39 rms-change max change #iterations 0.1601028 30.07178 at 10iterations 1.7020684E-02 2.331952 at 20iterations 1.7786004E-03 0.2712021 at 30iterations 2.1347436E-04 2.8686523E-02 at 40iterations 3.3266133E-05 5.5046082E-03 at 50iterations finished qdiffx linear iterations at : 14:39:42 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 3.3266133E-05 5.5046082E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 14:39:43 3.338u 0.166s 0:04.24 82.3% 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 14:39:43 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2377 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.973283 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): -22.75500 31.36800 ymin,ymax (A): 12.15600 58.13100 zmin,zma (A): 28.07900 78.25800 x,y,z range (A): 54.12300 45.97500 50.17900 scale (grids/A): 1.973283 object centre (A): 4.306500 35.14350 53.16850 number of atom coordinates read : 2377 total number of charged atoms : 2244 net assigned charge : -2.499994 assigned positive charge : 360.4772 centred at (gu) : 88.91099 92.22626 90.85671 assigned negative charge : -362.9778 centred at (gu) : 89.55550 92.14613 91.15521 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 74619 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20683 grid for indexing accessible points = 1.400000 m= 27857 mr = 51922 m= 5137 mr = 20801 m= 446 mr = 3435 m= 9 mr = 222 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1102 time to turn everything in is 0.3600000 number of dielectric boundary points 31688 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 17736 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) : 0.6577610 object centre at (A) : 4.306500 35.14350 53.16850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1501867E-02 -3.3107143E-02 midg,1,midg; midg,igrid,midg -1.0215458E-02 2.3605968E-03 1,midg,midg; igrid,midg,midg 4.5481499E-02 -1.0907196E-02 gauss-seidel spectral radius is 0.9987057 estimated iterations to convergence 220 setup time was (sec) 0.5800000 now iterating at: 14:39:44 rms-change max change #iterations 4.418809 198.0346 at 10iterations 2.106960 74.41851 at 20iterations 1.002336 31.73617 at 30iterations 0.4794269 14.05897 at 40iterations 0.2285555 7.623050 at 50iterations 0.1091936 3.540062 at 60iterations 5.2310951E-02 1.707703 at 70iterations 2.4973307E-02 0.7662735 at 80iterations 1.1942798E-02 0.3714752 at 90iterations 5.7212971E-03 0.2046700 at 100iterations 2.7380453E-03 9.0919495E-02 at 110iterations 1.3185370E-03 3.8473129E-02 at 120iterations finished qdiffx linear iterations at : 14:39:51 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 1.3185370E-03 3.8473129E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 14:39:51 7.725u 0.194s 0:08.37 94.5% 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 14:39:51 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2377 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.959924 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): -22.75500 31.36800 ymin,ymax (A): 12.15600 58.13100 zmin,zma (A): 28.07900 78.25800 x,y,z range (A): 54.12300 45.97500 50.17900 scale (grids/A): 2.959924 object centre (A): 4.306500 35.14350 53.16850 number of atom coordinates read : 2377 total number of charged atoms : 2244 net assigned charge : -2.499994 assigned positive charge : 360.4772 centred at (gu) : 88.36642 93.33935 91.28505 assigned negative charge : -362.9778 centred at (gu) : 89.33318 93.21911 91.73276 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 172676 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20683 grid for indexing accessible points = 1.400000 m= 88131 mr = 125849 m= 34220 mr = 72457 m= 9527 mr = 28024 m= 1863 mr = 7436 m= 173 mr = 1394 m= 7 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 3589 time to turn everything in is 0.9700000 number of dielectric boundary points 71352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 17951 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) : 1.973283 object centre at (A) : 4.306500 35.14350 53.16850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3359459 -0.1810497 midg,1,midg; midg,igrid,midg -3.9166018E-02 9.9797159E-02 1,midg,midg; igrid,midg,midg 0.5668526 -2.2688614E-02 gauss-seidel spectral radius is 0.9992694 estimated iterations to convergence 292 setup time was (sec) 1.200000 now iterating at: 14:39:53 rms-change max change #iterations 10.24533 444.0291 at 10iterations 6.004557 155.0869 at 20iterations 3.510425 84.81696 at 30iterations 2.046732 42.02438 at 40iterations 1.187679 22.01146 at 50iterations 0.6915482 13.50074 at 60iterations 0.3994759 8.227772 at 70iterations 0.2324388 4.290603 at 80iterations 0.1343097 2.598007 at 90iterations 7.7413879E-02 1.371593 at 100iterations 4.4876378E-02 0.8423005 at 110iterations 2.5884870E-02 0.4355431 at 120iterations 1.4965279E-02 0.2826337 at 130iterations 8.6334897E-03 0.1626657 at 140iterations 4.9942601E-03 9.7591400E-02 at 150iterations 2.8784384E-03 5.0663471E-02 at 160iterations 1.6663354E-03 3.0172825E-02 at 170iterations 9.6137921E-04 1.6670227E-02 at 180iterations finished qdiffx linear iterations at : 14:40:04 total time elapsed so far: 12.49000 # loops : 180 mean,max change (kT/e) : 9.6137921E-04 1.6670227E-02 energy calculations done at 12.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 14:40:05 12.629u 0.198s 0:13.40 95.5% 0+0k 0+0io 0pf+0w