Sat Oct 8 19:19:15 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 19:19:15 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2552 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 502 has a net charge of 1.4000 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: 0.7263379 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): -13.63400 35.37900 ymin,ymax (A): -26.92400 21.02600 zmin,zma (A): 32.88400 81.58100 x,y,z range (A): 49.01300 47.95000 48.69700 scale (grids/A): 0.7263379 object centre (A): 10.87250 -2.948999 57.23250 number of atom coordinates read : 2552 total number of charged atoms : 2444 net assigned charge : 4.000010 assigned positive charge : 389.8371 centred at (gu) : 90.05538 89.30628 90.22036 assigned negative charge : -385.8376 centred at (gu) : 90.03387 89.48197 90.18378 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 9339 nv = 96 ne = 84 npr = 52290 no. pairs analyzed = 52290 no. exposed pairs = 3020 no. arc points = 21700 no. surface atoms = 1022 nbur = 1530 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 653 mr = 5519 m= 5 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 208 time to turn everything in is 0.2100000 number of dielectric boundary points 4361 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1880 ## 156 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 10197 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6517140E-08 8.8147431E-08 midg,1,midg; midg,igrid,midg 2.4035262E-07 -9.9124868E-08 1,midg,midg; igrid,midg,midg 3.0779958E-08 7.1484791E-08 gauss-seidel spectral radius is 0.9901657 estimated iterations to convergence 82 setup time was (sec) 0.4300000 now iterating at: 19:19:15 rms-change max change #iterations 0.2511009 32.97240 at 10iterations 3.2587212E-02 4.923716 at 20iterations 4.2623477E-03 0.5245533 at 30iterations 5.6430732E-04 7.7860355E-02 at 40iterations 7.3014584E-05 8.6669922E-03 at 50iterations finished qdiffx linear iterations at : 19:19:18 total time elapsed so far: 3.660000 # loops : 50 mean,max change (kT/e) : 7.3014584E-05 8.6669922E-03 energy calculations done at 3.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.790000 DelPhi exited at 19:19:19 3.795u 0.201s 0:04.35 91.7% 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 19:19:19 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2552 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 502 has a net charge of 1.4000 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: 2.179014 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): -13.63400 35.37900 ymin,ymax (A): -26.92400 21.02600 zmin,zma (A): 32.88400 81.58100 x,y,z range (A): 49.01300 47.95000 48.69700 scale (grids/A): 2.179014 object centre (A): 10.87250 -2.948999 57.23250 number of atom coordinates read : 2552 total number of charged atoms : 2444 net assigned charge : 4.000010 assigned positive charge : 389.8371 centred at (gu) : 90.16585 87.91834 90.66074 assigned negative charge : -385.8376 centred at (gu) : 90.10149 88.44562 90.55113 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 98223 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21700 grid for indexing accessible points = 1.400000 m= 41353 mr = 70175 m= 8939 mr = 32366 m= 852 mr = 6212 m= 17 mr = 413 m= 0 mr = 3 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 5699 time to turn everything in is 0.4900000 number of dielectric boundary points 40215 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 19463 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) : 0.7263379 object centre at (A) : 10.87250 -2.948999 57.23250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0251520E-03 2.4219709E-02 midg,1,midg; midg,igrid,midg 6.7176379E-02 -2.7105376E-02 1,midg,midg; igrid,midg,midg -2.8499769E-02 9.8701948E-03 gauss-seidel spectral radius is 0.9989296 estimated iterations to convergence 242 setup time was (sec) 0.7300000 now iterating at: 19:19:20 rms-change max change #iterations 5.493979 201.1170 at 10iterations 2.798153 84.00446 at 20iterations 1.423385 43.07992 at 30iterations 0.7260966 20.05069 at 40iterations 0.3711611 11.88080 at 50iterations 0.1898980 5.036714 at 60iterations 9.6811898E-02 2.397924 at 70iterations 4.9510743E-02 1.395363 at 80iterations 2.5274800E-02 0.6555977 at 90iterations 1.2938721E-02 0.3784008 at 100iterations 6.6062668E-03 0.1819820 at 110iterations 3.3817918E-03 8.6517811E-02 at 120iterations finished qdiffx linear iterations at : 19:19:28 total time elapsed so far: 8.270000 # loops : 120 mean,max change (kT/e) : 3.3817918E-03 8.6517811E-02 energy calculations done at 8.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.400000 DelPhi exited at 19:19:28 8.403u 0.216s 0:08.89 96.8% 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 19:19:28 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2552 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 502 has a net charge of 1.4000 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: 3.268521 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): -13.63400 35.37900 ymin,ymax (A): -26.92400 21.02600 zmin,zma (A): 32.88400 81.58100 x,y,z range (A): 49.01300 47.95000 48.69700 scale (grids/A): 3.268521 object centre (A): 10.87250 -2.948999 57.23250 number of atom coordinates read : 2552 total number of charged atoms : 2444 net assigned charge : 4.000010 assigned positive charge : 389.8371 centred at (gu) : 90.24869 86.87741 90.99105 assigned negative charge : -385.8376 centred at (gu) : 90.15205 87.66833 90.82651 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 226066 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21700 grid for indexing accessible points = 1.400000 m= 126377 mr = 168120 m= 54967 mr = 107082 m= 17177 mr = 46338 m= 3604 mr = 13656 m= 396 mr = 2643 m= 15 mr = 232 m= 0 mr = 2 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 18484 time to turn everything in is 1.560000 number of dielectric boundary points 90529 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 19552 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) : 2.179014 object centre at (A) : 10.87250 -2.948999 57.23250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8891164E-02 0.5157672 midg,1,midg; midg,igrid,midg 0.4081085 -0.2247699 1,midg,midg; igrid,midg,midg -0.6839889 0.2110017 gauss-seidel spectral radius is 0.9993255 estimated iterations to convergence 304 setup time was (sec) 1.820000 now iterating at: 19:19:30 rms-change max change #iterations 11.85693 342.2614 at 10iterations 7.043522 136.1351 at 20iterations 4.168031 70.25325 at 30iterations 2.466220 44.62379 at 40iterations 1.460317 24.90887 at 50iterations 0.8619825 12.90359 at 60iterations 0.5092670 10.40273 at 70iterations 0.3006547 4.854395 at 80iterations 0.1773335 2.681366 at 90iterations 0.1045644 1.776769 at 100iterations 6.1791729E-02 0.9787312 at 110iterations 3.6462188E-02 0.5576248 at 120iterations 2.1538213E-02 0.3338852 at 130iterations 1.2706259E-02 0.1881332 at 140iterations 7.4928668E-03 0.1095409 at 150iterations 4.4365870E-03 7.8577042E-02 at 160iterations 2.6255557E-03 4.1193962E-02 at 170iterations 1.5617547E-03 2.4219513E-02 at 180iterations finished qdiffx linear iterations at : 19:19:43 total time elapsed so far: 14.35000 # loops : 180 mean,max change (kT/e) : 1.5617547E-03 2.4219513E-02 energy calculations done at 14.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.48000 DelPhi exited at 19:19:43 14.482u 0.235s 0:15.02 97.9% 0+0k 0+0io 0pf+0w