Sat Oct 8 11:43:41 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 11:43:41 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5310 !!! WARNING: GLM 242 has a net charge of -0.0940 !!! WARNING: HIR 314 has a net charge of 0.5140 !!! WARNING: HIR 344 has a net charge of 0.5140 !!! WARNING: HIR 470 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= 0.1700000 grid size : 179 scale,in grids/A, set to be: 0.5401223 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): 7.323000 72.97100 ymin,ymax (A): 4.596000 69.14200 zmin,zma (A): 9.408000 75.31900 x,y,z range (A): 65.64800 64.54600 65.91100 scale (grids/A): 0.5401223 object centre (A): 40.14700 36.86900 42.36350 number of atom coordinates read : 5310 total number of charged atoms : 5136 net assigned charge : 0.4480405 assigned positive charge : 807.5899 centred at (gu) : 90.20184 90.22281 91.24728 assigned negative charge : -807.1472 centred at (gu) : 90.13827 90.21144 91.28918 start vw surface at 0.2600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 9548 nv = 96 ne = 84 npr = 110679 no. pairs analyzed = 110679 no. exposed pairs = 6288 no. arc points = 42470 no. surface atoms = 2103 nbur = 3207 mkacc time = 0.3200000 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 = 1.596000 m= 378 mr = 5232 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 4675 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4330 ## 599 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 12932 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1301492E-10 -5.2432492E-10 midg,1,midg; midg,igrid,midg -7.9096667E-11 1.4362582E-10 1,midg,midg; igrid,midg,midg -5.6291755E-10 6.6842554E-10 gauss-seidel spectral radius is 0.9824923 estimated iterations to convergence 62 setup time was (sec) 0.9200000 now iterating at: 11:43:42 rms-change max change #iterations 9.4183728E-02 13.48337 at 10iterations 7.6347301E-03 1.322662 at 20iterations 1.2485863E-03 0.2949753 at 30iterations 3.2092008E-04 7.3104858E-02 at 40iterations 9.3093528E-05 1.8844604E-02 at 50iterations finished qdiffx linear iterations at : 11:43:45 total time elapsed so far: 4.110000 # loops : 50 mean,max change (kT/e) : 9.3093528E-05 1.8844604E-02 energy calculations done at 4.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.350000 DelPhi exited at 11:43:46 4.351u 0.167s 0:04.81 93.7% 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 11:43:46 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5310 !!! WARNING: GLM 242 has a net charge of -0.0940 !!! WARNING: HIR 314 has a net charge of 0.5140 !!! WARNING: HIR 344 has a net charge of 0.5140 !!! WARNING: HIR 470 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= 0.1700000 grid size : 179 scale,in grids/A, set to be: 1.620367 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): 7.323000 72.97100 ymin,ymax (A): 4.596000 69.14200 zmin,zma (A): 9.408000 75.31900 x,y,z range (A): 65.64800 64.54600 65.91100 scale (grids/A): 1.620367 object centre (A): 40.14700 36.86900 42.36350 number of atom coordinates read : 5310 total number of charged atoms : 5136 net assigned charge : 0.4480405 assigned positive charge : 807.5899 centred at (gu) : 90.60401 90.66673 93.74053 assigned negative charge : -807.1472 centred at (gu) : 90.41431 90.63403 93.86723 start vw surface at 0.2700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 108492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42470 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 33656 mr = 77156 m= 3495 mr = 23205 m= 83 mr = 1715 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 1493 time to turn everything in is 0.9500000 number of dielectric boundary points 43644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 508 ## 4 charges are in solution ## iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 39216 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) : 0.5401223 object centre at (A) : 40.14700 36.86900 42.36350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4343343E-02 -1.5098827E-03 midg,1,midg; midg,igrid,midg -7.4127284E-03 1.8150881E-02 1,midg,midg; igrid,midg,midg -1.1483689E-02 1.2023233E-02 gauss-seidel spectral radius is 0.9983720 estimated iterations to convergence 197 setup time was (sec) 1.300000 now iterating at: 11:43:47 rms-change max change #iterations 4.612391 154.5029 at 10iterations 2.009006 57.98907 at 20iterations 0.8781458 25.54938 at 30iterations 0.3842720 11.79499 at 40iterations 0.1687476 5.044630 at 50iterations 7.3798068E-02 2.117726 at 60iterations 3.2406148E-02 0.8781738 at 70iterations 1.4287925E-02 0.5174294 at 80iterations 6.3512502E-03 0.1766906 at 90iterations 2.8562630E-03 9.0560913E-02 at 100iterations 1.3198864E-03 4.3235779E-02 at 110iterations 6.4641866E-04 2.2811890E-02 at 120iterations finished qdiffx linear iterations at : 11:43:55 total time elapsed so far: 9.040000 # loops : 120 mean,max change (kT/e) : 6.4641866E-04 2.2811890E-02 energy calculations done at 9.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.270000 DelPhi exited at 11:43:55 9.277u 0.182s 0:09.73 97.1% 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 11:43:55 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5310 !!! WARNING: GLM 242 has a net charge of -0.0940 !!! WARNING: HIR 314 has a net charge of 0.5140 !!! WARNING: HIR 344 has a net charge of 0.5140 !!! WARNING: HIR 470 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= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.430550 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): 7.323000 72.97100 ymin,ymax (A): 4.596000 69.14200 zmin,zma (A): 9.408000 75.31900 x,y,z range (A): 65.64800 64.54600 65.91100 scale (grids/A): 2.430550 object centre (A): 40.14700 36.86900 42.36350 number of atom coordinates read : 5310 total number of charged atoms : 5136 net assigned charge : 0.4480405 assigned positive charge : 807.5899 centred at (gu) : 90.90578 90.99976 95.61035 assigned negative charge : -807.1472 centred at (gu) : 90.62142 90.95113 95.80074 start vw surface at 0.2500000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 253494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42470 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 117139 mr = 189373 m= 33479 mr = 93279 m= 5287 mr = 25151 m= 312 mr = 3400 m= 3 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 1.390000 no. cavity mid-points inaccessible to solvent = 5093 time to turn everything in is 2.320000 number of dielectric boundary points 98403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 2.490000 number of grid points assigned charge 41037 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) : 1.620367 object centre at (A) : 40.14700 36.86900 42.36350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2001693 -0.3357745 midg,1,midg; midg,igrid,midg -0.1263939 0.1970637 1,midg,midg; igrid,midg,midg -0.2505908 4.8079398E-02 gauss-seidel spectral radius is 0.9992446 estimated iterations to convergence 287 setup time was (sec) 2.680000 now iterating at: 11:43:58 rms-change max change #iterations 12.11255 309.6660 at 10iterations 7.211879 166.5575 at 20iterations 4.263483 92.63478 at 30iterations 2.508557 48.34886 at 40iterations 1.467815 31.91912 at 50iterations 0.8570292 19.20198 at 60iterations 0.4981710 9.381075 at 70iterations 0.2892202 5.080123 at 80iterations 0.1673024 3.143436 at 90iterations 9.6786425E-02 1.686546 at 100iterations 5.6052800E-02 1.104942 at 110iterations 3.2368436E-02 0.6692514 at 120iterations 1.8718634E-02 0.3712578 at 130iterations 1.0803916E-02 0.1940823 at 140iterations 6.2711397E-03 0.1151247 at 150iterations 3.6396189E-03 7.4542999E-02 at 160iterations 2.1261887E-03 4.0359497E-02 at 170iterations 1.2577967E-03 2.4024963E-02 at 180iterations finished qdiffx linear iterations at : 11:44:11 total time elapsed so far: 15.03000 # loops : 180 mean,max change (kT/e) : 1.2577967E-03 2.4024963E-02 energy calculations done at 15.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.27000 DelPhi exited at 11:44:11 15.272u 0.214s 0:15.95 97.0% 0+0k 0+0io 0pf+0w