Sun Oct 9 08:10:29 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 08:10:29 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4029 !!! WARNING: GLM 214 has a net charge of -0.0940 !!! WARNING: NDP 1056 has a net charge of -3.0000 !!! WARNING: NDP 1059 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.4810421 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): -25.17300 24.70500 ymin,ymax (A): -22.11600 51.89000 zmin,zma (A): -16.83200 49.92900 x,y,z range (A): 49.87800 74.00600 66.76100 scale (grids/A): 0.4810421 object centre (A): -0.2340002 14.88700 16.54850 number of atom coordinates read : 4029 total number of charged atoms : 3881 net assigned charge : 7.906045 assigned positive charge : 611.9352 centred at (gu) : 89.51221 85.33789 89.24011 assigned negative charge : -604.0321 centred at (gu) : 89.63408 85.46464 89.12921 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6001 nv = 96 ne = 84 npr = 78066 no. pairs analyzed = 78066 no. exposed pairs = 5528 no. arc points = 39620 no. surface atoms = 1830 nbur = 2199 mkacc time = 0.2200000 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 = 1.764000 m= 187 mr = 2806 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 3382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3715 ## 644 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 8146 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.8881517E-11 6.8082318E-11 midg,1,midg; midg,igrid,midg 3.5291306E-10 -1.2990583E-11 1,midg,midg; igrid,midg,midg 1.0307340E-10 -3.9478143E-11 gauss-seidel spectral radius is 0.9778779 estimated iterations to convergence 56 setup time was (sec) 0.7300000 now iterating at: 08:10:30 rms-change max change #iterations 4.4721130E-02 9.223740 at 10iterations 2.2143635E-03 0.3913460 at 20iterations 2.4534282E-04 3.4961939E-02 at 30iterations 6.1741259E-05 8.3808899E-03 at 40iterations 1.7013712E-05 2.3393631E-03 at 50iterations finished qdiffx linear iterations at : 08:10:33 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 1.7013712E-05 2.3393631E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 08:10:33 4.212u 0.272s 0:04.75 94.3% 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 08:10:34 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4029 !!! WARNING: GLM 214 has a net charge of -0.0940 !!! WARNING: NDP 1056 has a net charge of -3.0000 !!! WARNING: NDP 1059 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.443126 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): -25.17300 24.70500 ymin,ymax (A): -22.11600 51.89000 zmin,zma (A): -16.83200 49.92900 x,y,z range (A): 49.87800 74.00600 66.76100 scale (grids/A): 1.443126 object centre (A): -0.2340002 14.88700 16.54850 number of atom coordinates read : 4029 total number of charged atoms : 3881 net assigned charge : 7.906045 assigned positive charge : 611.9352 centred at (gu) : 88.53538 76.01252 87.71959 assigned negative charge : -604.0321 centred at (gu) : 88.90176 76.39375 87.38770 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 68672 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39620 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 17169 mr = 44365 m= 1161 mr = 10371 m= 23 mr = 387 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 57 time to turn everything in is 0.6300000 number of dielectric boundary points 31902 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 551 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 28565 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) : 0.4810421 object centre at (A) : -0.2340002 14.88700 16.54850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5678434E-03 5.4332898E-03 midg,1,midg; midg,igrid,midg 2.0853687E-02 8.8491628E-04 1,midg,midg; igrid,midg,midg 5.5949423E-03 -6.0326362E-04 gauss-seidel spectral radius is 0.9977503 estimated iterations to convergence 168 setup time was (sec) 0.9400000 now iterating at: 08:10:35 rms-change max change #iterations 2.982312 153.6284 at 10iterations 1.127360 56.36270 at 20iterations 0.4252336 16.57177 at 30iterations 0.1608481 7.067001 at 40iterations 6.0445882E-02 2.603308 at 50iterations 2.2990841E-02 0.9015903 at 60iterations 8.6802617E-03 0.3479433 at 70iterations 3.3187021E-03 0.1370001 at 80iterations 1.2935991E-03 5.0622702E-02 at 90iterations 5.2103947E-04 2.0087242E-02 at 100iterations 2.2697392E-04 8.1517696E-03 at 110iterations 1.1148000E-04 3.9482117E-03 at 120iterations finished qdiffx linear iterations at : 08:10:43 total time elapsed so far: 9.160000 # loops : 120 mean,max change (kT/e) : 1.1148000E-04 3.9482117E-03 energy calculations done at 9.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.330000 DelPhi exited at 08:10:43 9.330u 0.290s 0:09.88 97.3% 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 08:10:43 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4029 !!! WARNING: GLM 214 has a net charge of -0.0940 !!! WARNING: NDP 1056 has a net charge of -3.0000 !!! WARNING: NDP 1059 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.164689 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): -25.17300 24.70500 ymin,ymax (A): -22.11600 51.89000 zmin,zma (A): -16.83200 49.92900 x,y,z range (A): 49.87800 74.00600 66.76100 scale (grids/A): 2.164689 object centre (A): -0.2340002 14.88700 16.54850 number of atom coordinates read : 4029 total number of charged atoms : 3881 net assigned charge : 7.906045 assigned positive charge : 611.9352 centred at (gu) : 87.80291 69.01863 86.57915 assigned negative charge : -604.0321 centred at (gu) : 88.35244 69.59053 86.08136 start vw surface at 0.2000000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 160483 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39620 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 64027 mr = 110504 m= 13421 mr = 47293 m= 1415 mr = 8873 m= 46 mr = 734 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 190 time to turn everything in is 1.490000 number of dielectric boundary points 71984 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 30865 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) : 1.443126 object centre at (A) : -0.2340002 14.88700 16.54850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1512893 0.1117041 midg,1,midg; midg,igrid,midg 0.6133376 4.8573937E-02 1,midg,midg; igrid,midg,midg 7.7410519E-02 -2.1464320E-02 gauss-seidel spectral radius is 0.9990121 estimated iterations to convergence 252 setup time was (sec) 1.810000 now iterating at: 08:10:46 rms-change max change #iterations 8.532783 371.5758 at 10iterations 4.661419 135.0759 at 20iterations 2.523449 66.18858 at 30iterations 1.358559 35.92704 at 40iterations 0.7256563 18.52373 at 50iterations 0.3876218 10.85210 at 60iterations 0.2061518 5.276237 at 70iterations 0.1096089 2.956367 at 80iterations 5.8021754E-02 1.576935 at 90iterations 3.0685654E-02 0.7863312 at 100iterations 1.6275119E-02 0.4164429 at 110iterations 8.6063230E-03 0.1975718 at 120iterations 4.5349775E-03 0.1062832 at 130iterations 2.4064400E-03 6.1888695E-02 at 140iterations 1.2677778E-03 3.2615662E-02 at 150iterations 6.7128916E-04 1.6176224E-02 at 160iterations 3.5551426E-04 8.3503723E-03 at 170iterations 1.8859662E-04 4.5614243E-03 at 180iterations finished qdiffx linear iterations at : 08:10:59 total time elapsed so far: 15.31000 # loops : 180 mean,max change (kT/e) : 1.8859662E-04 4.5614243E-03 energy calculations done at 15.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.49000 DelPhi exited at 08:11:00 15.494u 0.302s 0:16.06 98.3% 0+0k 0+0io 0pf+0w