Tue Oct 11 03:21:46 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 03:21:46 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 = 2469 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5929380 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): -25.85000 24.23000 ymin,ymax (A): -1.692000 54.73800 zmin,zma (A): -35.49400 24.54600 x,y,z range (A): 50.08000 56.43000 60.04000 scale (grids/A): 0.5929380 object centre (A): -0.8100004 26.52300 -5.474002 number of atom coordinates read : 2469 total number of charged atoms : 2323 net assigned charge : 2.500014 assigned positive charge : 364.8291 centred at (gu) : 88.63728 92.27639 92.47278 assigned negative charge : -362.3299 centred at (gu) : 88.57571 92.11870 92.33660 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5839 nv = 96 ne = 84 npr = 48383 no. pairs analyzed = 48383 no. exposed pairs = 3259 no. arc points = 23941 no. surface atoms = 1099 nbur = 1370 mkacc time = 0.1300000 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 = 1.456000 m= 249 mr = 2891 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 48 time to turn everything in is 0.3300000 number of dielectric boundary points 3186 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2369 ## 264 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7204 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7199783E-09 7.6179631E-09 midg,1,midg; midg,igrid,midg -2.1537094E-09 8.2279801E-09 1,midg,midg; igrid,midg,midg -1.4117967E-09 1.6884072E-09 gauss-seidel spectral radius is 0.9852805 estimated iterations to convergence 68 setup time was (sec) 0.6100000 now iterating at: 03:21:47 rms-change max change #iterations 9.6629575E-02 15.33430 at 10iterations 7.8563793E-03 1.383201 at 20iterations 6.5232418E-04 0.1084715 at 30iterations 5.2789263E-05 9.0100765E-03 at 40iterations 4.4157014E-06 6.6375732E-04 at 50iterations finished qdiffx linear iterations at : 03:21:50 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 4.4157014E-06 6.6375732E-04 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 03:21:51 4.139u 0.245s 0:04.72 92.5% 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 Tue Oct 11 2011 at 03:21:51 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 = 2469 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: 1.778814 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): -25.85000 24.23000 ymin,ymax (A): -1.692000 54.73800 zmin,zma (A): -35.49400 24.54600 x,y,z range (A): 50.08000 56.43000 60.04000 scale (grids/A): 1.778814 object centre (A): -0.8100004 26.52300 -5.474002 number of atom coordinates read : 2469 total number of charged atoms : 2323 net assigned charge : 2.500014 assigned positive charge : 364.8291 centred at (gu) : 85.91151 96.82894 97.41786 assigned negative charge : -362.3299 centred at (gu) : 85.72711 96.35596 97.00964 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 62982 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23941 grid for indexing accessible points = 1.400000 m= 20159 mr = 40831 m= 2489 mr = 14202 m= 107 mr = 1382 m= 0 mr = 21 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 770 time to turn everything in is 0.5700000 number of dielectric boundary points 29301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 18090 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) : 0.5929380 object centre at (A) : -0.8100004 26.52300 -5.474002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8816165E-03 3.3527408E-02 midg,1,midg; midg,igrid,midg -6.6816839E-03 2.2317301E-02 1,midg,midg; igrid,midg,midg -5.6010636E-04 3.8629284E-03 gauss-seidel spectral radius is 0.9984235 estimated iterations to convergence 200 setup time was (sec) 0.8600000 now iterating at: 03:21:52 rms-change max change #iterations 3.549104 183.8381 at 10iterations 1.560484 83.90643 at 20iterations 0.6887692 25.55543 at 30iterations 0.3037152 10.60706 at 40iterations 0.1335733 4.441106 at 50iterations 5.9033480E-02 2.183290 at 60iterations 2.6178019E-02 0.9944935 at 70iterations 1.1516814E-02 0.4101291 at 80iterations 5.0839055E-03 0.1843853 at 90iterations 2.2512532E-03 7.7972412E-02 at 100iterations 9.9632051E-04 3.3949852E-02 at 110iterations 4.4138616E-04 1.5480042E-02 at 120iterations finished qdiffx linear iterations at : 03:22:00 total time elapsed so far: 9.250000 # loops : 120 mean,max change (kT/e) : 4.4138616E-04 1.5480042E-02 energy calculations done at 9.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.420000 DelPhi exited at 03:22:01 9.426u 0.329s 0:10.08 96.6% 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 03:22:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2469 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: 2.668221 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): -25.85000 24.23000 ymin,ymax (A): -1.692000 54.73800 zmin,zma (A): -35.49400 24.54600 x,y,z range (A): 50.08000 56.43000 60.04000 scale (grids/A): 2.668221 object centre (A): -0.8100004 26.52300 -5.474002 number of atom coordinates read : 2469 total number of charged atoms : 2323 net assigned charge : 2.500014 assigned positive charge : 364.8291 centred at (gu) : 83.86707 100.2433 101.1268 assigned negative charge : -362.3299 centred at (gu) : 83.59063 99.53393 100.5144 start vw surface at 0.1600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 145985 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23941 grid for indexing accessible points = 1.400000 m= 66918 mr = 99919 m= 21530 mr = 53124 m= 4058 mr = 16713 m= 417 mr = 2814 m= 16 mr = 239 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 2396 time to turn everything in is 1.400000 number of dielectric boundary points 66115 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 18577 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) : 1.778814 object centre at (A) : -0.8100004 26.52300 -5.474002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1258669E-02 0.5576666 midg,1,midg; midg,igrid,midg -4.9865521E-02 0.2051834 1,midg,midg; igrid,midg,midg -2.7366059E-02 4.2601611E-02 gauss-seidel spectral radius is 0.9991970 estimated iterations to convergence 279 setup time was (sec) 1.720000 now iterating at: 03:22:03 rms-change max change #iterations 8.672175 289.3360 at 10iterations 4.960083 135.3389 at 20iterations 2.806636 68.24493 at 30iterations 1.583174 38.48990 at 40iterations 0.8925593 21.94371 at 50iterations 0.5030035 13.15745 at 60iterations 0.2824128 5.899971 at 70iterations 0.1583921 3.455199 at 80iterations 8.9080982E-02 1.922987 at 90iterations 5.0006058E-02 1.074341 at 100iterations 2.8021576E-02 0.5786604 at 110iterations 1.5724545E-02 0.3432026 at 120iterations 8.8264598E-03 0.1866302 at 130iterations 4.9396614E-03 0.1101570 at 140iterations 2.7748782E-03 6.0751915E-02 at 150iterations 1.5627797E-03 3.2472610E-02 at 160iterations 8.7315234E-04 1.7184734E-02 at 170iterations 4.9212482E-04 1.1057377E-02 at 180iterations finished qdiffx linear iterations at : 03:22:16 total time elapsed so far: 15.41000 # loops : 180 mean,max change (kT/e) : 4.9212482E-04 1.1057377E-02 energy calculations done at 15.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.59000 DelPhi exited at 03:22:17 15.588u 0.323s 0:16.22 98.0% 0+0k 0+0io 0pf+0w