Sat Oct 8 15:55:59 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 Sat Oct 8 2011 at 15:55:59 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2362 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 !!! WARNING: HIR 874 has a net charge of 0.5140 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: 0.5842962 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): -2.244000 44.85100 ymin,ymax (A): -15.36800 29.93800 zmin,zma (A): -19.24200 41.68600 x,y,z range (A): 47.09500 45.30600 60.92800 scale (grids/A): 0.5842962 object centre (A): 21.30350 7.285000 11.22200 number of atom coordinates read : 2362 total number of charged atoms : 2281 net assigned charge : 3.820002 assigned positive charge : 354.3060 centred at (gu) : 90.65732 88.70315 88.94498 assigned negative charge : -350.4868 centred at (gu) : 90.69221 88.83357 88.96906 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5246 nv = 96 ne = 84 npr = 48093 no. pairs analyzed = 48093 no. exposed pairs = 2972 no. arc points = 20530 no. surface atoms = 1010 nbur = 1352 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= 231 mr = 2810 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.3300000 number of dielectric boundary points 2649 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2102 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 6818 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7941184E-09 3.5814021E-10 midg,1,midg; midg,igrid,midg 4.7342996E-09 -1.2511969E-09 1,midg,midg; igrid,midg,midg 1.3948724E-09 2.5999242E-10 gauss-seidel spectral radius is 0.9848263 estimated iterations to convergence 67 setup time was (sec) 0.6000000 now iterating at: 15:56:00 rms-change max change #iterations 9.0293787E-02 15.07328 at 10iterations 7.2254450E-03 1.350983 at 20iterations 6.3570740E-04 9.7732544E-02 at 30iterations 8.2710940E-05 1.5540600E-02 at 40iterations 1.8156121E-05 3.8609505E-03 at 50iterations finished qdiffx linear iterations at : 15:56:03 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 1.8156121E-05 3.8609505E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 15:56:04 4.188u 0.296s 0:04.80 93.1% 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 Sat Oct 8 2011 at 15:56:04 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2362 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 !!! WARNING: HIR 874 has a net charge of 0.5140 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: 1.752889 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): -2.244000 44.85100 ymin,ymax (A): -15.36800 29.93800 zmin,zma (A): -19.24200 41.68600 x,y,z range (A): 47.09500 45.30600 60.92800 scale (grids/A): 1.752889 object centre (A): 21.30350 7.285000 11.22200 number of atom coordinates read : 2362 total number of charged atoms : 2281 net assigned charge : 3.820002 assigned positive charge : 354.3060 centred at (gu) : 91.97166 86.10869 86.83457 assigned negative charge : -350.4868 centred at (gu) : 92.07662 86.50046 86.90704 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 57775 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20530 grid for indexing accessible points = 1.400000 m= 18346 mr = 39613 m= 2320 mr = 13004 m= 73 mr = 1381 m= 0 mr = 7 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 995 time to turn everything in is 0.5400000 number of dielectric boundary points 24509 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 173 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 17710 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) : 0.5842962 object centre at (A) : 21.30350 7.285000 11.22200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6945032E-02 1.3126864E-02 midg,1,midg; midg,igrid,midg 1.3621460E-02 -3.2985930E-03 1,midg,midg; igrid,midg,midg 3.3279546E-03 -1.6482972E-02 gauss-seidel spectral radius is 0.9983614 estimated iterations to convergence 196 setup time was (sec) 0.8500000 now iterating at: 15:56:05 rms-change max change #iterations 3.395747 153.4850 at 10iterations 1.484472 53.49976 at 20iterations 0.6478271 23.39067 at 30iterations 0.2835666 10.67029 at 40iterations 0.1236336 4.711465 at 50iterations 5.3969998E-02 2.159137 at 60iterations 2.3690214E-02 0.8358450 at 70iterations 1.0289306E-02 0.4058647 at 80iterations 4.4935378E-03 0.1668358 at 90iterations 1.9670660E-03 7.0552826E-02 at 100iterations 8.6595339E-04 3.0164719E-02 at 110iterations 3.8212442E-04 1.3907909E-02 at 120iterations finished qdiffx linear iterations at : 15:56:13 total time elapsed so far: 9.340000 # loops : 120 mean,max change (kT/e) : 3.8212442E-04 1.3907909E-02 energy calculations done at 9.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.540000 DelPhi exited at 15:56:14 9.538u 0.322s 0:10.23 96.2% 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 Sat Oct 8 2011 at 15:56:14 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2362 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 !!! WARNING: HIR 874 has a net charge of 0.5140 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: 2.629333 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): -2.244000 44.85100 ymin,ymax (A): -15.36800 29.93800 zmin,zma (A): -19.24200 41.68600 x,y,z range (A): 47.09500 45.30600 60.92800 scale (grids/A): 2.629333 object centre (A): 21.30350 7.285000 11.22200 number of atom coordinates read : 2362 total number of charged atoms : 2281 net assigned charge : 3.820002 assigned positive charge : 354.3060 centred at (gu) : 92.95730 84.16295 85.25181 assigned negative charge : -350.4868 centred at (gu) : 93.11487 84.75063 85.36062 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 134312 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20530 grid for indexing accessible points = 1.400000 m= 62254 mr = 96917 m= 19638 mr = 49789 m= 3882 mr = 15389 m= 321 mr = 2896 m= 11 mr = 175 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 3451 time to turn everything in is 1.300000 number of dielectric boundary points 55252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 18240 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) : 1.752889 object centre at (A) : 21.30350 7.285000 11.22200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2284936 0.3958899 midg,1,midg; midg,igrid,midg 0.1456404 -4.1155491E-02 1,midg,midg; igrid,midg,midg 4.7360405E-02 -0.2617141 gauss-seidel spectral radius is 0.9991758 estimated iterations to convergence 275 setup time was (sec) 1.640000 now iterating at: 15:56:16 rms-change max change #iterations 8.425615 290.9864 at 10iterations 4.778118 123.0818 at 20iterations 2.698871 68.62273 at 30iterations 1.520810 32.68885 at 40iterations 0.8549164 19.76178 at 50iterations 0.4804132 9.919985 at 60iterations 0.2691268 5.568840 at 70iterations 0.1507963 3.082493 at 80iterations 8.4203243E-02 2.180763 at 90iterations 4.6934344E-02 0.9354372 at 100iterations 2.6313659E-02 0.5785236 at 110iterations 1.4690045E-02 0.3238020 at 120iterations 8.1975032E-03 0.1634803 at 130iterations 4.5712497E-03 9.8214149E-02 at 140iterations 2.5547813E-03 6.2682152E-02 at 150iterations 1.4271587E-03 3.2161713E-02 at 160iterations 8.0019794E-04 1.7528534E-02 at 170iterations 4.5080460E-04 8.9583397E-03 at 180iterations finished qdiffx linear iterations at : 15:56:30 total time elapsed so far: 15.48000 # loops : 180 mean,max change (kT/e) : 4.5080460E-04 8.9583397E-03 energy calculations done at 15.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.67000 DelPhi exited at 15:56:31 15.670u 0.327s 0:16.53 96.7% 0+0k 0+0io 0pf+0w