Mon Oct 10 17:04:26 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 Mon Oct 10 2011 at 17:04:26 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4751 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5136418 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): -17.95000 36.97500 ymin,ymax (A): -31.18000 31.59200 zmin,zma (A): -4.008000 65.30100 x,y,z range (A): 54.92500 62.77200 69.30901 scale (grids/A): 0.5136418 object centre (A): 9.512502 0.2059994 30.64650 number of atom coordinates read : 4751 total number of charged atoms : 4505 net assigned charge : 5.800029 assigned positive charge : 712.4404 centred at (gu) : 90.16058 91.03798 88.41687 assigned negative charge : -706.6450 centred at (gu) : 90.04523 91.09695 88.41430 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7893 nv = 96 ne = 84 npr = 95930 no. pairs analyzed = 95930 no. exposed pairs = 6046 no. arc points = 41723 no. surface atoms = 2032 nbur = 2719 mkacc time = 0.1700000 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 = 1.652000 m= 283 mr = 4036 m= 3 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4136 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4009 ## 564 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 10510 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3209990E-10 6.8997433E-11 midg,1,midg; midg,igrid,midg 2.0277188E-10 -1.0361812E-10 1,midg,midg; igrid,midg,midg -2.3467794E-10 4.4430831E-10 gauss-seidel spectral radius is 0.9806136 estimated iterations to convergence 59 setup time was (sec) 0.5300000 now iterating at: 17:04:27 rms-change max change #iterations 6.9591098E-02 9.173084 at 10iterations 4.1403603E-03 0.6586323 at 20iterations 4.3134362E-04 6.0432434E-02 at 30iterations 1.5147576E-04 2.4757743E-02 at 40iterations 6.4787353E-05 1.1413574E-02 at 50iterations finished qdiffx linear iterations at : 17:04:30 total time elapsed so far: 3.580000 # loops : 50 mean,max change (kT/e) : 6.4787353E-05 1.1413574E-02 energy calculations done at 3.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 17:04:31 3.714u 0.189s 0:04.73 82.2% 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 Mon Oct 10 2011 at 17:04:31 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4751 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.540925 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): -17.95000 36.97500 ymin,ymax (A): -31.18000 31.59200 zmin,zma (A): -4.008000 65.30100 x,y,z range (A): 54.92500 62.77200 69.30901 scale (grids/A): 1.540925 object centre (A): 9.512502 0.2059994 30.64650 number of atom coordinates read : 4751 total number of charged atoms : 4505 net assigned charge : 5.800029 assigned positive charge : 712.4404 centred at (gu) : 90.48036 93.11250 85.24918 assigned negative charge : -706.6450 centred at (gu) : 90.13511 93.29067 85.24260 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 89940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41723 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26394 mr = 61976 m= 2283 mr = 17299 m= 54 mr = 882 m= 0 mr = 3 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.4500000 number of dielectric boundary points 38511 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 516 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 33890 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) : 0.5136418 object centre at (A) : 9.512502 0.2059994 30.64650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0292412E-03 1.6639274E-02 midg,1,midg; midg,igrid,midg 1.3163941E-02 -1.5195066E-02 1,midg,midg; igrid,midg,midg -1.0385214E-03 1.1544231E-02 gauss-seidel spectral radius is 0.9981354 estimated iterations to convergence 184 setup time was (sec) 0.6800000 now iterating at: 17:04:32 rms-change max change #iterations 3.843479 175.2233 at 10iterations 1.577973 48.88424 at 20iterations 0.6499061 20.15491 at 30iterations 0.2684686 8.883737 at 40iterations 0.1108464 3.575157 at 50iterations 4.5876767E-02 1.646080 at 60iterations 1.8903967E-02 0.5994644 at 70iterations 7.8482497E-03 0.2473412 at 80iterations 3.2564993E-03 0.1011314 at 90iterations 1.3659841E-03 4.5372009E-02 at 100iterations 5.9240567E-04 2.0186901E-02 at 110iterations 2.7495390E-04 9.5233917E-03 at 120iterations finished qdiffx linear iterations at : 17:04:40 total time elapsed so far: 8.270000 # loops : 120 mean,max change (kT/e) : 2.7495390E-04 9.5233917E-03 energy calculations done at 8.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.420000 DelPhi exited at 17:04:40 8.420u 0.221s 0:08.97 96.3% 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 Mon Oct 10 2011 at 17:04:40 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4751 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.311388 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): -17.95000 36.97500 ymin,ymax (A): -31.18000 31.59200 zmin,zma (A): -4.008000 65.30100 x,y,z range (A): 54.92500 62.77200 69.30901 scale (grids/A): 2.311388 object centre (A): 9.512502 0.2059994 30.64650 number of atom coordinates read : 4751 total number of charged atoms : 4505 net assigned charge : 5.800029 assigned positive charge : 712.4404 centred at (gu) : 90.72031 94.66830 82.87328 assigned negative charge : -706.6450 centred at (gu) : 90.20242 94.93582 82.86379 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 209953 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41723 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 94225 mr = 152424 m= 23672 mr = 73280 m= 3197 mr = 16650 m= 179 mr = 1829 m= 4 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 102 time to turn everything in is 1.060000 number of dielectric boundary points 86998 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 35938 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) : 1.540925 object centre at (A) : 9.512502 0.2059994 30.64650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1203870 0.4438554 midg,1,midg; midg,igrid,midg 0.2906918 -0.3590091 1,midg,midg; igrid,midg,midg -1.6971998E-02 0.1564570 gauss-seidel spectral radius is 0.9991695 estimated iterations to convergence 274 setup time was (sec) 1.310000 now iterating at: 17:04:42 rms-change max change #iterations 10.33160 338.8919 at 10iterations 5.921356 135.7642 at 20iterations 3.379508 73.13811 at 30iterations 1.911766 38.49032 at 40iterations 1.078527 25.10822 at 50iterations 0.6077820 12.90097 at 60iterations 0.3410856 6.762985 at 70iterations 0.1912795 4.191056 at 80iterations 0.1070587 1.966925 at 90iterations 5.9851695E-02 1.099222 at 100iterations 3.3417314E-02 0.6730528 at 110iterations 1.8669864E-02 0.3767920 at 120iterations 1.0434555E-02 0.2065392 at 130iterations 5.8139274E-03 0.1100769 at 140iterations 3.2523482E-03 6.0899734E-02 at 150iterations 1.8236394E-03 3.4954071E-02 at 160iterations 1.0320091E-03 2.4589539E-02 at 170iterations 5.9239904E-04 1.1474609E-02 at 180iterations finished qdiffx linear iterations at : 17:04:54 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 5.9239904E-04 1.1474609E-02 energy calculations done at 13.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 17:04:55 13.234u 0.227s 0:14.35 93.7% 0+0k 0+0io 0pf+0w