Tue Oct 11 08:22:31 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 Tue Oct 11 2011 at 08:22:31 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2826 !!! WARNING: HIQ 72 has a net charge of 0.5140 !!! WARNING: SEP 226 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6065252 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): -12.84600 36.95200 ymin,ymax (A): -26.94800 21.48100 zmin,zma (A): -13.28900 45.40600 x,y,z range (A): 49.79800 48.42900 58.69500 scale (grids/A): 0.6065252 object centre (A): 12.05300 -2.733500 16.05850 number of atom coordinates read : 2826 total number of charged atoms : 2669 net assigned charge : -1.320983 assigned positive charge : 430.2278 centred at (gu) : 90.47039 90.51647 92.46138 assigned negative charge : -431.5492 centred at (gu) : 90.20259 90.39433 92.33397 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6757 nv = 96 ne = 84 npr = 58331 no. pairs analyzed = 58331 no. exposed pairs = 3322 no. arc points = 23342 no. surface atoms = 1119 nbur = 1707 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 306 mr = 3791 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3200000 number of dielectric boundary points 3256 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2383 ## 263 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8468 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2046984E-09 9.3213997E-09 midg,1,midg; midg,igrid,midg -6.2625030E-09 5.6207923E-09 1,midg,midg; igrid,midg,midg -1.3063633E-08 1.3202039E-08 gauss-seidel spectral radius is 0.9859407 estimated iterations to convergence 69 setup time was (sec) 0.5400000 now iterating at: 08:22:32 rms-change max change #iterations 0.1236387 24.30312 at 10iterations 1.1204707E-02 1.701225 at 20iterations 1.1703906E-03 0.1532784 at 30iterations 2.0366992E-04 2.6702881E-02 at 40iterations 5.6153352E-05 8.5096359E-03 at 50iterations finished qdiffx linear iterations at : 08:22:35 total time elapsed so far: 3.720000 # loops : 50 mean,max change (kT/e) : 5.6153352E-05 8.5096359E-03 energy calculations done at 3.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.900000 DelPhi exited at 08:22:36 3.904u 0.188s 0:04.54 89.8% 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 Tue Oct 11 2011 at 08:22:36 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2826 !!! WARNING: HIQ 72 has a net charge of 0.5140 !!! WARNING: SEP 226 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.819576 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): -12.84600 36.95200 ymin,ymax (A): -26.94800 21.48100 zmin,zma (A): -13.28900 45.40600 x,y,z range (A): 49.79800 48.42900 58.69500 scale (grids/A): 1.819576 object centre (A): 12.05300 -2.733500 16.05850 number of atom coordinates read : 2826 total number of charged atoms : 2669 net assigned charge : -1.320983 assigned positive charge : 430.2278 centred at (gu) : 91.41048 91.54890 97.38358 assigned negative charge : -431.5492 centred at (gu) : 90.60763 91.18272 97.00167 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 73654 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23342 grid for indexing accessible points = 1.400000 m= 25897 mr = 51847 m= 3384 mr = 19289 m= 121 mr = 1957 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 936 time to turn everything in is 0.5500000 number of dielectric boundary points 29939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 206 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 20866 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) : 0.6065252 object centre at (A) : 12.05300 -2.733500 16.05850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.7667916E-02 1.6877790E-04 midg,1,midg; midg,igrid,midg -1.0560507E-02 1.2882924E-02 1,midg,midg; igrid,midg,midg -8.6707771E-03 3.6451161E-02 gauss-seidel spectral radius is 0.9985234 estimated iterations to convergence 206 setup time was (sec) 0.8200000 now iterating at: 08:22:37 rms-change max change #iterations 4.130864 218.8217 at 10iterations 1.876399 70.49530 at 20iterations 0.8542715 27.21885 at 30iterations 0.3873892 14.55252 at 40iterations 0.1771829 5.670303 at 50iterations 8.0645800E-02 3.316620 at 60iterations 3.6817163E-02 1.086761 at 70iterations 1.6787369E-02 0.5809898 at 80iterations 7.7173393E-03 0.2431545 at 90iterations 3.5654895E-03 0.1301050 at 100iterations 1.6762980E-03 5.0979614E-02 at 110iterations 8.0550543E-04 3.0364990E-02 at 120iterations finished qdiffx linear iterations at : 08:22:43 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 8.0550543E-04 3.0364990E-02 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.560000 DelPhi exited at 08:22:44 7.559u 0.248s 0:08.34 93.4% 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 Tue Oct 11 2011 at 08:22:44 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2826 !!! WARNING: HIQ 72 has a net charge of 0.5140 !!! WARNING: SEP 226 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.729363 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): -12.84600 36.95200 ymin,ymax (A): -26.94800 21.48100 zmin,zma (A): -13.28900 45.40600 x,y,z range (A): 49.79800 48.42900 58.69500 scale (grids/A): 2.729363 object centre (A): 12.05300 -2.733500 16.05850 number of atom coordinates read : 2826 total number of charged atoms : 2669 net assigned charge : -1.320983 assigned positive charge : 430.2278 centred at (gu) : 92.11566 92.32317 101.0752 assigned negative charge : -431.5492 centred at (gu) : 90.91129 91.77406 100.5023 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 170739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23342 grid for indexing accessible points = 1.400000 m= 85999 mr = 125782 m= 28536 mr = 70860 m= 5672 mr = 22785 m= 593 mr = 4155 m= 22 mr = 348 m= 0 mr = 2 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 3079 time to turn everything in is 1.250000 number of dielectric boundary points 67629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 21346 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) : 1.819576 object centre at (A) : 12.05300 -2.733500 16.05850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.367035 0.1155841 midg,1,midg; midg,igrid,midg -0.1273997 0.1687279 1,midg,midg; igrid,midg,midg -7.4930027E-02 0.3385654 gauss-seidel spectral radius is 0.9992268 estimated iterations to convergence 284 setup time was (sec) 1.530000 now iterating at: 08:22:46 rms-change max change #iterations 9.797754 289.8370 at 10iterations 5.639635 136.2012 at 20iterations 3.232457 67.59531 at 30iterations 1.851136 36.46039 at 40iterations 1.053580 21.04763 at 50iterations 0.6020751 11.67827 at 60iterations 0.3432440 6.318241 at 70iterations 0.1956651 3.938726 at 80iterations 0.1112930 2.231141 at 90iterations 6.3399509E-02 1.143091 at 100iterations 3.6081746E-02 0.6519294 at 110iterations 2.0553390E-02 0.3880692 at 120iterations 1.1718160E-02 0.2109222 at 130iterations 6.7158947E-03 0.1191902 at 140iterations 3.8650506E-03 8.7142944E-02 at 150iterations 2.2470881E-03 4.0008545E-02 at 160iterations 1.3249768E-03 2.6138306E-02 at 170iterations 7.9657510E-04 1.6429901E-02 at 180iterations finished qdiffx linear iterations at : 08:22:56 total time elapsed so far: 11.34000 # loops : 180 mean,max change (kT/e) : 7.9657510E-04 1.6429901E-02 energy calculations done at 11.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.53000 DelPhi exited at 08:22:56 11.532u 0.196s 0:12.10 96.8% 0+0k 0+0io 0pf+0w