Tue Oct 11 06:33:01 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 Tue Oct 11 2011 at 06:33:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7071068 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): -18.74100 25.25800 ymin,ymax (A): -28.58100 11.08400 zmin,zma (A): -13.69600 36.65000 x,y,z range (A): 43.99900 39.66500 50.34600 scale (grids/A): 0.7071068 object centre (A): 3.258501 -8.748501 11.47700 number of atom coordinates read : 2089 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 89.36653 90.64111 89.28971 assigned negative charge : -311.0742 centred at (gu) : 89.22640 90.61436 89.21922 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7018 nv = 96 ne = 84 npr = 42287 no. pairs analyzed = 42287 no. exposed pairs = 2509 no. arc points = 16977 no. surface atoms = 856 nbur = 1233 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 434 mr = 4059 m= 8 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.2800000 number of dielectric boundary points 3326 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1665 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7911 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2984501E-08 7.7931709E-08 midg,1,midg; midg,igrid,midg 3.7315566E-08 7.7009908E-08 1,midg,midg; igrid,midg,midg -1.6794692E-08 1.0847078E-07 gauss-seidel spectral radius is 0.9895727 estimated iterations to convergence 80 setup time was (sec) 0.5500000 now iterating at: 06:33:02 rms-change max change #iterations 0.1984341 25.99494 at 10iterations 2.4876235E-02 3.534085 at 20iterations 3.1387166E-03 0.4309487 at 30iterations 4.5190571E-04 6.3055038E-02 at 40iterations 8.7276530E-05 1.3126373E-02 at 50iterations finished qdiffx linear iterations at : 06:33:05 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 8.7276530E-05 1.3126373E-02 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 06:33:06 4.034u 0.297s 0:04.80 90.0% 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 06:33:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 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: 2.121320 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): -18.74100 25.25800 ymin,ymax (A): -28.58100 11.08400 zmin,zma (A): -13.69600 36.65000 x,y,z range (A): 43.99900 39.66500 50.34600 scale (grids/A): 2.121320 object centre (A): 3.258501 -8.748501 11.47700 number of atom coordinates read : 2089 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 88.09956 91.92339 87.86904 assigned negative charge : -311.0742 centred at (gu) : 87.67931 91.84327 87.65766 start vw surface at 0.1500000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 74976 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16977 grid for indexing accessible points = 1.400000 m= 29579 mr = 53747 m= 5614 mr = 22435 m= 534 mr = 3777 m= 21 mr = 294 m= 0 mr = 5 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 285 time to turn everything in is 0.6900000 number of dielectric boundary points 30466 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 15579 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) : 0.7071068 object centre at (A) : 3.258501 -8.748501 11.47700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3210167E-02 4.3649144E-02 midg,1,midg; midg,igrid,midg 5.5503962E-03 3.4832388E-02 1,midg,midg; igrid,midg,midg 1.9239621E-02 3.1854421E-02 gauss-seidel spectral radius is 0.9988275 estimated iterations to convergence 231 setup time was (sec) 1.000000 now iterating at: 06:33:07 rms-change max change #iterations 4.605555 218.4838 at 10iterations 2.276659 82.27795 at 20iterations 1.129353 34.53948 at 30iterations 0.5578800 17.21639 at 40iterations 0.2768285 8.702882 at 50iterations 0.1373733 4.019241 at 60iterations 6.8185829E-02 2.008997 at 70iterations 3.3826929E-02 1.040814 at 80iterations 1.6866338E-02 0.4949145 at 90iterations 8.3861919E-03 0.2521572 at 100iterations 4.1855108E-03 0.1207504 at 110iterations 2.0986877E-03 6.4512253E-02 at 120iterations finished qdiffx linear iterations at : 06:33:15 total time elapsed so far: 9.300000 # loops : 120 mean,max change (kT/e) : 2.0986877E-03 6.4512253E-02 energy calculations done at 9.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.480000 DelPhi exited at 06:33:16 9.483u 0.280s 0:10.03 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 Tue Oct 11 2011 at 06:33:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.181981 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): -18.74100 25.25800 ymin,ymax (A): -28.58100 11.08400 zmin,zma (A): -13.69600 36.65000 x,y,z range (A): 43.99900 39.66500 50.34600 scale (grids/A): 3.181981 object centre (A): 3.258501 -8.748501 11.47700 number of atom coordinates read : 2089 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 87.14939 92.88506 86.80358 assigned negative charge : -311.0742 centred at (gu) : 86.51889 92.76492 86.48653 start vw surface at 0.1500000 fill in re-entrant regions at 0.9800000 boundary points on vw surface= 172880 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16977 grid for indexing accessible points = 1.400000 m= 92854 mr = 129195 m= 37073 mr = 77387 m= 10707 mr = 30525 m= 2173 mr = 8330 m= 290 mr = 1592 m= 19 mr = 213 m= 0 mr = 13 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 917 time to turn everything in is 2.190000 number of dielectric boundary points 68741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.340000 number of grid points assigned charge 15687 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) : 2.121320 object centre at (A) : 3.258501 -8.748501 11.47700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7381154 0.3778812 midg,1,midg; midg,igrid,midg 2.9149672E-02 0.2945729 1,midg,midg; igrid,midg,midg 0.4274579 0.2863018 gauss-seidel spectral radius is 0.9992928 estimated iterations to convergence 297 setup time was (sec) 2.510000 now iterating at: 06:33:19 rms-change max change #iterations 10.21949 402.1762 at 10iterations 6.030355 125.3423 at 20iterations 3.543986 70.91521 at 30iterations 2.084939 36.84573 at 40iterations 1.222943 21.75171 at 50iterations 0.7180194 15.19098 at 60iterations 0.4204023 7.522565 at 70iterations 0.2460830 4.664894 at 80iterations 0.1438468 2.726291 at 90iterations 8.4244005E-02 1.502580 at 100iterations 4.9287185E-02 0.8821936 at 110iterations 2.8950205E-02 0.5317993 at 120iterations 1.7027404E-02 0.3338356 at 130iterations 1.0118910E-02 0.2005157 at 140iterations 6.0953833E-03 0.1140327 at 150iterations 3.7497978E-03 6.8374634E-02 at 160iterations 2.4077632E-03 4.5791626E-02 at 170iterations 1.6216038E-03 3.0370712E-02 at 180iterations finished qdiffx linear iterations at : 06:33:32 total time elapsed so far: 16.17000 # loops : 180 mean,max change (kT/e) : 1.6216038E-03 3.0370712E-02 energy calculations done at 16.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.36000 DelPhi exited at 06:33:33 16.358u 0.310s 0:17.09 97.4% 0+0k 0+0io 0pf+0w