Sun Oct 9 08:09:57 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 08:09:57 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4029 !!! 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 : 3885 net assigned charge : 8.000043 assigned positive charge : 611.4952 centred at (gu) : 89.51025 85.33805 89.23941 assigned negative charge : -603.4981 centred at (gu) : 89.63069 85.46425 89.13029 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 8149 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7147862E-11 6.7518380E-11 midg,1,midg; midg,igrid,midg 3.5273554E-10 -1.2789726E-11 1,midg,midg; igrid,midg,midg 1.0256020E-10 -3.8399839E-11 gauss-seidel spectral radius is 0.9778779 estimated iterations to convergence 56 setup time was (sec) 0.7400000 now iterating at: 08:09:58 rms-change max change #iterations 4.4499423E-02 9.224327 at 10iterations 2.1982456E-03 0.3911781 at 20iterations 2.4177028E-04 3.4704685E-02 at 30iterations 6.1120183E-05 8.3192587E-03 at 40iterations 1.6863223E-05 2.3187995E-03 at 50iterations finished qdiffx linear iterations at : 08:10:02 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 1.6863223E-05 2.3187995E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 08:10:02 4.245u 0.254s 0:04.96 90.5% 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 08:10:02 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4029 !!! 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 : 3885 net assigned charge : 8.000043 assigned positive charge : 611.4952 centred at (gu) : 88.52951 76.01301 87.71748 assigned negative charge : -603.4981 centred at (gu) : 88.89160 76.39259 87.39098 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 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 0.6400000 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 28593 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 -7.5005856E-03 5.4221568E-03 midg,1,midg; midg,igrid,midg 2.0682769E-02 8.9110847E-04 1,midg,midg; igrid,midg,midg 5.5963323E-03 -4.9100228E-04 gauss-seidel spectral radius is 0.9977503 estimated iterations to convergence 168 setup time was (sec) 0.9400000 now iterating at: 08:10:04 rms-change max change #iterations 2.977876 153.6284 at 10iterations 1.125171 56.36269 at 20iterations 0.4243164 16.57178 at 30iterations 0.1604702 7.067001 at 40iterations 6.0317006E-02 2.521166 at 50iterations 2.2930263E-02 0.9014111 at 60iterations 8.6565409E-03 0.3456726 at 70iterations 3.3097093E-03 0.1356106 at 80iterations 1.2883779E-03 5.1051140E-02 at 90iterations 5.1773508E-04 2.0423889E-02 at 100iterations 2.2471794E-04 8.1691742E-03 at 110iterations 1.0971943E-04 3.8151741E-03 at 120iterations finished qdiffx linear iterations at : 08:10:12 total time elapsed so far: 9.170000 # loops : 120 mean,max change (kT/e) : 1.0971943E-04 3.8151741E-03 energy calculations done at 9.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.360000 DelPhi exited at 08:10:12 9.359u 0.272s 0:10.00 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 Sun Oct 9 2011 at 08:10:12 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4029 !!! 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 : 3885 net assigned charge : 8.000043 assigned positive charge : 611.4952 centred at (gu) : 87.79412 69.01936 86.57599 assigned negative charge : -603.4981 centred at (gu) : 88.33721 69.58879 86.08629 start vw surface at 0.2000000 fill in re-entrant regions at 0.5000000 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 1.630000 number of grid points assigned charge 30897 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 -0.1500769 0.1115613 midg,1,midg; midg,igrid,midg 0.6095133 4.8697088E-02 1,midg,midg; igrid,midg,midg 7.7462330E-02 -1.9268537E-02 gauss-seidel spectral radius is 0.9990121 estimated iterations to convergence 252 setup time was (sec) 1.810000 now iterating at: 08:10:14 rms-change max change #iterations 8.521316 371.5758 at 10iterations 4.656092 135.0752 at 20iterations 2.520284 66.30827 at 30iterations 1.357229 35.83081 at 40iterations 0.7248520 18.41438 at 50iterations 0.3872203 11.05432 at 60iterations 0.2059555 5.293797 at 70iterations 0.1095060 2.934559 at 80iterations 5.7968751E-02 1.572929 at 90iterations 3.0657640E-02 0.7836380 at 100iterations 1.6260954E-02 0.4178600 at 110iterations 8.5980436E-03 0.1968889 at 120iterations 4.5312378E-03 0.1070910 at 130iterations 2.4049422E-03 6.1817169E-02 at 140iterations 1.2667369E-03 3.2989502E-02 at 150iterations 6.7068788E-04 1.6539574E-02 at 160iterations 3.5529718E-04 8.4152222E-03 at 170iterations 1.8844011E-04 4.5795441E-03 at 180iterations finished qdiffx linear iterations at : 08:10:28 total time elapsed so far: 15.32000 # loops : 180 mean,max change (kT/e) : 1.8844011E-04 4.5795441E-03 energy calculations done at 15.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.50000 DelPhi exited at 08:10:28 15.498u 0.318s 0:16.08 98.2% 0+0k 0+0io 0pf+0w