Sun Oct 9 08:18:07 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 Sun Oct 9 2011 at 08:18:07 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 = 5614 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5182101 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): -31.50200 27.91500 ymin,ymax (A): -13.44400 54.88500 zmin,zma (A): -32.07900 36.61900 x,y,z range (A): 59.41700 68.32899 68.69801 scale (grids/A): 0.5182101 object centre (A): -1.793500 20.72050 2.270000 number of atom coordinates read : 5614 total number of charged atoms : 5444 net assigned charge : -4.999987 assigned positive charge : 840.7206 centred at (gu) : 87.97296 90.03437 89.78825 assigned negative charge : -845.7275 centred at (gu) : 87.95097 89.93575 89.85744 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 9518 nv = 96 ne = 84 npr = 114307 no. pairs analyzed = 114307 no. exposed pairs = 7039 no. arc points = 48700 no. surface atoms = 2361 nbur = 3253 mkacc time = 0.2900000 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 = 1.652000 m= 338 mr = 4964 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 4886 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4712 ## 621 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 12732 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0278226E-10 -3.7022760E-10 midg,1,midg; midg,igrid,midg -5.1333771E-10 3.1563371E-10 1,midg,midg; igrid,midg,midg -3.2277023E-10 -4.2401868E-12 gauss-seidel spectral radius is 0.9810117 estimated iterations to convergence 60 setup time was (sec) 0.8500000 now iterating at: 08:18:08 rms-change max change #iterations 7.9091750E-02 12.32704 at 10iterations 4.9727187E-03 0.6818390 at 20iterations 6.0449826E-04 0.1286793 at 30iterations 1.7575177E-04 3.9443970E-02 at 40iterations 5.8171285E-05 1.2521744E-02 at 50iterations finished qdiffx linear iterations at : 08:18:12 total time elapsed so far: 4.690000 # loops : 50 mean,max change (kT/e) : 5.8171285E-05 1.2521744E-02 energy calculations done at 4.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.890000 DelPhi exited at 08:18:13 4.893u 0.408s 0:05.57 94.9% 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 Sun Oct 9 2011 at 08:18:13 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 = 5614 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.554630 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): -31.50200 27.91500 ymin,ymax (A): -13.44400 54.88500 zmin,zma (A): -32.07900 36.61900 x,y,z range (A): 59.41700 68.32899 68.69801 scale (grids/A): 1.554630 object centre (A): -1.793500 20.72050 2.270000 number of atom coordinates read : 5614 total number of charged atoms : 5444 net assigned charge : -4.999987 assigned positive charge : 840.7206 centred at (gu) : 83.91688 90.10119 89.36264 assigned negative charge : -845.7275 centred at (gu) : 83.85258 89.80685 89.57190 start vw surface at 0.2000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 107340 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48700 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 31213 mr = 73910 m= 2719 mr = 20717 m= 64 mr = 1225 m= 0 mr = 4 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 1079 time to turn everything in is 0.9000000 number of dielectric boundary points 45480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 619 ## 5 charges are in solution ## iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 41066 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) : 0.5182101 object centre at (A) : -1.793500 20.72050 2.270000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2913117E-03 -8.9398492E-03 midg,1,midg; midg,igrid,midg -3.2721173E-03 8.6578624E-03 1,midg,midg; igrid,midg,midg -1.3039218E-03 -6.1156374E-04 gauss-seidel spectral radius is 0.9982475 estimated iterations to convergence 190 setup time was (sec) 1.200000 now iterating at: 08:18:14 rms-change max change #iterations 4.308422 153.6449 at 10iterations 1.827930 54.95565 at 20iterations 0.7755355 23.14988 at 30iterations 0.3282662 9.559757 at 40iterations 0.1391675 4.186871 at 50iterations 5.9005532E-02 1.830769 at 60iterations 2.5177546E-02 0.7796264 at 70iterations 1.0698119E-02 0.3039284 at 80iterations 4.5867781E-03 0.1317444 at 90iterations 1.9910985E-03 6.3937187E-02 at 100iterations 8.7643455E-04 2.9340744E-02 at 110iterations 4.1069920E-04 1.6511917E-02 at 120iterations finished qdiffx linear iterations at : 08:18:24 total time elapsed so far: 11.07000 # loops : 120 mean,max change (kT/e) : 4.1069920E-04 1.6511917E-02 energy calculations done at 11.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.24000 DelPhi exited at 08:18:25 11.243u 0.479s 0:12.01 97.5% 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 Sun Oct 9 2011 at 08:18:25 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 = 5614 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.331945 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): -31.50200 27.91500 ymin,ymax (A): -13.44400 54.88500 zmin,zma (A): -32.07900 36.61900 x,y,z range (A): 59.41700 68.32899 68.69801 scale (grids/A): 2.331945 object centre (A): -1.793500 20.72050 2.270000 number of atom coordinates read : 5614 total number of charged atoms : 5444 net assigned charge : -4.999987 assigned positive charge : 840.7206 centred at (gu) : 80.87481 90.15115 89.04343 assigned negative charge : -845.7275 centred at (gu) : 80.77875 89.71030 89.35785 start vw surface at 0.1900000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 250295 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48700 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 111790 mr = 181783 m= 28450 mr = 87172 m= 3884 mr = 20411 m= 225 mr = 2409 m= 2 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 1.380000 no. cavity mid-points inaccessible to solvent = 3997 time to turn everything in is 2.200000 number of dielectric boundary points 102787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 2.370000 number of grid points assigned charge 43436 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) : 1.554630 object centre at (A) : -1.793500 20.72050 2.270000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2743703 9.9735916E-02 midg,1,midg; midg,igrid,midg -6.1599426E-02 0.1318643 1,midg,midg; igrid,midg,midg 5.8949441E-02 -1.0388381E-02 gauss-seidel spectral radius is 0.9992288 estimated iterations to convergence 284 setup time was (sec) 2.570000 now iterating at: 08:18:28 rms-change max change #iterations 11.64812 266.1045 at 10iterations 6.883529 147.2254 at 20iterations 4.039443 81.25795 at 30iterations 2.350039 45.01256 at 40iterations 1.364043 27.08462 at 50iterations 0.7886496 14.77674 at 60iterations 0.4554186 7.542629 at 70iterations 0.2618246 4.603634 at 80iterations 0.1503080 2.618961 at 90iterations 8.6342156E-02 1.495831 at 100iterations 4.9483191E-02 0.8285179 at 110iterations 2.8316120E-02 0.5028324 at 120iterations 1.6221799E-02 0.2832651 at 130iterations 9.2887888E-03 0.1628222 at 140iterations 5.3138984E-03 8.9742661E-02 at 150iterations 3.0526801E-03 5.0509974E-02 at 160iterations 1.7577307E-03 2.9224396E-02 at 170iterations 1.0217360E-03 1.6281128E-02 at 180iterations finished qdiffx linear iterations at : 08:18:45 total time elapsed so far: 19.86000 # loops : 180 mean,max change (kT/e) : 1.0217360E-03 1.6281128E-02 energy calculations done at 19.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.04000 DelPhi exited at 08:18:46 20.042u 0.493s 0:21.01 97.7% 0+0k 0+0io 0pf+0w