Sun Oct 9 07:57:29 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+sph2.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 = amb2.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 07:57:29 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2215 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 0.6927014 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): 4.651000 50.21600 ymin,ymax (A): -24.96900 26.42400 zmin,zma (A): -18.55900 30.29300 x,y,z range (A): 45.56500 51.39300 48.85200 scale (grids/A): 0.6927014 object centre (A): 27.43350 0.7275000 5.867001 number of atom coordinates read : 2215 total number of charged atoms : 2073 net assigned charge : -3.499990 assigned positive charge : 338.5374 centred at (gu) : 90.01120 90.95395 89.79743 assigned negative charge : -342.0377 centred at (gu) : 90.03037 91.05072 89.88786 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7384 nv = 96 ne = 84 npr = 44197 no. pairs analyzed = 44197 no. exposed pairs = 2819 no. arc points = 20388 no. surface atoms = 944 nbur = 1271 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 510 mr = 4079 m= 10 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.1800000 number of dielectric boundary points 3719 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1899 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8191 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5033384E-08 -5.3461317E-08 midg,1,midg; midg,igrid,midg 1.3650161E-08 -7.0427284E-08 1,midg,midg; igrid,midg,midg -1.2883525E-08 -2.7818682E-08 gauss-seidel spectral radius is 0.9891645 estimated iterations to convergence 78 setup time was (sec) 0.3700000 now iterating at: 07:57:30 rms-change max change #iterations 0.1967326 26.58579 at 10iterations 2.3374023E-02 3.044064 at 20iterations 2.7454537E-03 0.3823719 at 30iterations 3.2383029E-04 4.6646118E-02 at 40iterations 3.7889833E-05 5.5203438E-03 at 50iterations finished qdiffx linear iterations at : 07:57:33 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 3.7889833E-05 5.5203438E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 07:57:34 3.429u 0.531s 0:04.29 92.0% 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 07:57:34 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2215 !!! WARNING: NDP 385 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.078104 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): 4.651000 50.21600 ymin,ymax (A): -24.96900 26.42400 zmin,zma (A): -18.55900 30.29300 x,y,z range (A): 45.56500 51.39300 48.85200 scale (grids/A): 2.078104 object centre (A): 27.43350 0.7275000 5.867001 number of atom coordinates read : 2215 total number of charged atoms : 2073 net assigned charge : -3.499990 assigned positive charge : 338.5374 centred at (gu) : 90.03343 92.86157 89.39187 assigned negative charge : -342.0377 centred at (gu) : 90.09097 93.15222 89.66357 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77610 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20388 grid for indexing accessible points = 1.400000 m= 30965 mr = 53341 m= 6442 mr = 23341 m= 605 mr = 4411 m= 23 mr = 282 m= 0 mr = 6 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 451 time to turn everything in is 0.4100000 number of dielectric boundary points 34264 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 16445 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) : 0.6927014 object centre at (A) : 27.43350 0.7275000 5.867001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0270765E-02 -3.4399189E-02 midg,1,midg; midg,igrid,midg 2.6697058E-02 -1.4658207E-02 1,midg,midg; igrid,midg,midg -2.3604748E-03 -3.1037321E-02 gauss-seidel spectral radius is 0.9988137 estimated iterations to convergence 230 setup time was (sec) 0.6400000 now iterating at: 07:57:35 rms-change max change #iterations 4.721630 178.3578 at 10iterations 2.313278 71.10497 at 20iterations 1.141331 36.65863 at 30iterations 0.5619875 16.11987 at 40iterations 0.2765939 9.086308 at 50iterations 0.1366974 4.195755 at 60iterations 6.7267999E-02 1.934898 at 70iterations 3.3222035E-02 1.072306 at 80iterations 1.6275482E-02 0.4703827 at 90iterations 8.0402633E-03 0.2787170 at 100iterations 3.9557740E-03 0.1301041 at 110iterations 1.9532414E-03 6.0709000E-02 at 120iterations finished qdiffx linear iterations at : 07:57:42 total time elapsed so far: 8.520000 # loops : 120 mean,max change (kT/e) : 1.9532414E-03 6.0709000E-02 energy calculations done at 8.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.660000 DelPhi exited at 07:57:43 8.666u 0.228s 0:09.25 96.0% 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 07:57:43 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2215 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 3.117156 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): 4.651000 50.21600 ymin,ymax (A): -24.96900 26.42400 zmin,zma (A): -18.55900 30.29300 x,y,z range (A): 45.56500 51.39300 48.85200 scale (grids/A): 3.117156 object centre (A): 27.43350 0.7275000 5.867001 number of atom coordinates read : 2215 total number of charged atoms : 2073 net assigned charge : -3.499990 assigned positive charge : 338.5374 centred at (gu) : 90.05006 94.29236 89.08772 assigned negative charge : -342.0377 centred at (gu) : 90.13650 94.72842 89.49534 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 178571 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20388 grid for indexing accessible points = 1.400000 m= 95281 mr = 128247 m= 40314 mr = 78720 m= 12197 mr = 33334 m= 2577 mr = 9563 m= 275 mr = 1864 m= 21 mr = 134 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 1455 time to turn everything in is 1.250000 number of dielectric boundary points 77364 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 16584 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) : 2.078104 object centre at (A) : 27.43350 0.7275000 5.867001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1854697 -0.2634780 midg,1,midg; midg,igrid,midg 0.7871203 -3.7681997E-02 1,midg,midg; igrid,midg,midg -5.5094834E-02 -0.2959817 gauss-seidel spectral radius is 0.9992977 estimated iterations to convergence 298 setup time was (sec) 1.500000 now iterating at: 07:57:45 rms-change max change #iterations 10.60740 422.1226 at 10iterations 6.224473 122.4248 at 20iterations 3.633989 73.93970 at 30iterations 2.126082 49.06839 at 40iterations 1.244340 21.76859 at 50iterations 0.7257110 14.69170 at 60iterations 0.4241879 7.643406 at 70iterations 0.2470792 5.066154 at 80iterations 0.1439035 2.512802 at 90iterations 8.4074296E-02 1.403584 at 100iterations 4.8907530E-02 0.8674326 at 110iterations 2.8578339E-02 0.4749756 at 120iterations 1.6618583E-02 0.2828274 at 130iterations 9.6803857E-03 0.1685791 at 140iterations 5.6463671E-03 9.9693298E-02 at 150iterations 3.2921727E-03 5.8811188E-02 at 160iterations 1.9185278E-03 3.4630775E-02 at 170iterations 1.1217566E-03 1.8758297E-02 at 180iterations finished qdiffx linear iterations at : 07:57:58 total time elapsed so far: 13.41000 # loops : 180 mean,max change (kT/e) : 1.1217566E-03 1.8758297E-02 energy calculations done at 13.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.55000 DelPhi exited at 07:57:58 13.548u 1.282s 0:15.13 97.9% 0+0k 0+0io 0pf+0w