Sat Oct 15 15:13:06 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 Sat Oct 15 2011 at 15:13:06 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 = 2779 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: 0.6698781 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): -11.65700 37.43100 ymin,ymax (A): -28.91300 21.57100 zmin,zma (A): -7.637000 45.50700 x,y,z range (A): 49.08800 50.48400 53.14400 scale (grids/A): 0.6698781 object centre (A): 12.88700 -3.671000 18.93500 number of atom coordinates read : 2779 total number of charged atoms : 2631 net assigned charge : 5.500014 assigned positive charge : 423.7008 centred at (gu) : 89.98072 90.34595 90.90422 assigned negative charge : -418.2014 centred at (gu) : 89.70750 90.17313 90.99595 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8462 nv = 96 ne = 84 npr = 55660 no. pairs analyzed = 55660 no. exposed pairs = 3464 no. arc points = 24292 no. surface atoms = 1158 nbur = 1621 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 503 mr = 4766 m= 6 mr = 99 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.2100000 number of dielectric boundary points 4106 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2289 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9821 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6010121E-08 -8.5650944E-09 midg,1,midg; midg,igrid,midg -2.7529117E-08 6.9652366E-08 1,midg,midg; igrid,midg,midg -5.8685469E-08 9.0687159E-08 gauss-seidel spectral radius is 0.9884654 estimated iterations to convergence 76 setup time was (sec) 0.4000000 now iterating at: 15:13:07 rms-change max change #iterations 0.1819359 24.43114 at 10iterations 2.0660402E-02 2.697862 at 20iterations 2.3081929E-03 0.2750893 at 30iterations 2.7366658E-04 3.4879684E-02 at 40iterations 3.9932413E-05 5.6886673E-03 at 50iterations finished qdiffx linear iterations at : 15:13:11 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 3.9932413E-05 5.6886673E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 15:13:11 3.549u 0.185s 0:05.16 72.0% 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 Sat Oct 15 2011 at 15:13:11 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 = 2779 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: 2.009634 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): -11.65700 37.43100 ymin,ymax (A): -28.91300 21.57100 zmin,zma (A): -7.637000 45.50700 x,y,z range (A): 49.08800 50.48400 53.14400 scale (grids/A): 2.009634 object centre (A): 12.88700 -3.671000 18.93500 number of atom coordinates read : 2779 total number of charged atoms : 2631 net assigned charge : 5.500014 assigned positive charge : 423.7008 centred at (gu) : 89.94187 91.03735 92.71181 assigned negative charge : -418.2014 centred at (gu) : 89.12241 90.51891 92.98757 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 89847 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24292 grid for indexing accessible points = 1.400000 m= 35381 mr = 62836 m= 6373 mr = 26895 m= 415 mr = 4195 m= 9 mr = 183 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1065 time to turn everything in is 0.4200000 number of dielectric boundary points 37916 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 20795 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) : 0.6698781 object centre at (A) : 12.88700 -3.671000 18.93500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8614996E-02 -2.1772616E-02 midg,1,midg; midg,igrid,midg -1.1678298E-02 5.6189530E-02 1,midg,midg; igrid,midg,midg -1.0906546E-02 8.6151004E-02 gauss-seidel spectral radius is 0.9987895 estimated iterations to convergence 228 setup time was (sec) 0.6400000 now iterating at: 15:13:12 rms-change max change #iterations 4.891453 199.9602 at 10iterations 2.402041 90.05841 at 20iterations 1.175179 32.47944 at 30iterations 0.5770127 16.69790 at 40iterations 0.2825655 7.597836 at 50iterations 0.1385651 3.689888 at 60iterations 6.8000309E-02 1.852112 at 70iterations 3.3267614E-02 0.9544239 at 80iterations 1.6317979E-02 0.5411019 at 90iterations 7.9907617E-03 0.2273550 at 100iterations 3.9216820E-03 0.1063795 at 110iterations 1.9312355E-03 5.4132462E-02 at 120iterations finished qdiffx linear iterations at : 15:13:25 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 1.9312355E-03 5.4132462E-02 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.070000 DelPhi exited at 15:13:26 8.077u 0.219s 0:14.17 58.4% 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 Sat Oct 15 2011 at 15:13:26 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2779 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: 3.014451 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): -11.65700 37.43100 ymin,ymax (A): -28.91300 21.57100 zmin,zma (A): -7.637000 45.50700 x,y,z range (A): 49.08800 50.48400 53.14400 scale (grids/A): 3.014451 object centre (A): 12.88700 -3.671000 18.93500 number of atom coordinates read : 2779 total number of charged atoms : 2631 net assigned charge : 5.500014 assigned positive charge : 423.7008 centred at (gu) : 89.91257 91.55588 94.06757 assigned negative charge : -418.2014 centred at (gu) : 88.68359 90.77824 94.48129 start vw surface at 0.1000000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 207121 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24292 grid for indexing accessible points = 1.400000 m= 110719 mr = 151343 m= 44675 mr = 92078 m= 11978 mr = 36828 m= 1933 mr = 9304 m= 141 mr = 1353 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 3555 time to turn everything in is 1.170000 number of dielectric boundary points 85599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 21048 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) : 2.009634 object centre at (A) : 12.88700 -3.671000 18.93500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2081922 5.5665493E-02 midg,1,midg; midg,igrid,midg -0.1528710 0.5897372 1,midg,midg; igrid,midg,midg -4.2437337E-02 0.7012073 gauss-seidel spectral radius is 0.9992973 estimated iterations to convergence 298 setup time was (sec) 1.420000 now iterating at: 15:13:27 rms-change max change #iterations 11.20965 385.2317 at 10iterations 6.619293 152.0738 at 20iterations 3.905397 73.09185 at 30iterations 2.297858 41.22298 at 40iterations 1.351192 21.59141 at 50iterations 0.7914513 13.42830 at 60iterations 0.4633804 7.923996 at 70iterations 0.2715328 4.715887 at 80iterations 0.1590820 2.872026 at 90iterations 9.2993975E-02 1.565496 at 100iterations 5.4322250E-02 0.8930640 at 110iterations 3.1833913E-02 0.5405617 at 120iterations 1.8618710E-02 0.3337288 at 130iterations 1.0894803E-02 0.1722488 at 140iterations 6.3910778E-03 0.1016621 at 150iterations 3.7514691E-03 6.0806274E-02 at 160iterations 2.2147305E-03 3.9013863E-02 at 170iterations 1.3146754E-03 2.2958755E-02 at 180iterations finished qdiffx linear iterations at : 15:13:39 total time elapsed so far: 13.11000 # loops : 180 mean,max change (kT/e) : 1.3146754E-03 2.2958755E-02 energy calculations done at 13.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.24000 DelPhi exited at 15:13:40 13.242u 0.206s 0:13.89 96.7% 0+0k 0+0io 0pf+0w