Sun Oct 9 23:23:16 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 Sun Oct 9 2011 at 23:23:16 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2266 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: 0.6686575 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): -11.99500 32.68800 ymin,ymax (A): -22.29400 28.44100 zmin,zma (A): -10.54500 42.69600 x,y,z range (A): 44.68300 50.73500 53.24100 scale (grids/A): 0.6686575 object centre (A): 10.34650 3.073501 16.07550 number of atom coordinates read : 2266 total number of charged atoms : 2127 net assigned charge : 1.500010 assigned positive charge : 336.9995 centred at (gu) : 91.76357 91.04374 90.18570 assigned negative charge : -335.4998 centred at (gu) : 91.71204 90.91141 89.96287 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7021 nv = 96 ne = 84 npr = 44507 no. pairs analyzed = 44507 no. exposed pairs = 2976 no. arc points = 21136 no. surface atoms = 1011 nbur = 1255 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 388 mr = 3712 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1969 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8039 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2466361E-08 5.2392743E-08 midg,1,midg; midg,igrid,midg -1.9445666E-08 3.9699653E-08 1,midg,midg; igrid,midg,midg -4.6216053E-09 2.1800126E-08 gauss-seidel spectral radius is 0.9883850 estimated iterations to convergence 76 setup time was (sec) 0.5700000 now iterating at: 23:23:17 rms-change max change #iterations 0.1624801 24.59729 at 10iterations 1.8130017E-02 2.525253 at 20iterations 1.9725128E-03 0.2945709 at 30iterations 2.6915091E-04 4.3484688E-02 at 40iterations 7.7456250E-05 1.4943004E-02 at 50iterations finished qdiffx linear iterations at : 23:23:20 total time elapsed so far: 3.760000 # loops : 50 mean,max change (kT/e) : 7.7456250E-05 1.4943004E-02 energy calculations done at 3.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 23:23:21 3.931u 0.255s 0:04.59 91.0% 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 Sun Oct 9 2011 at 23:23:21 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2266 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: 2.005973 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): -11.99500 32.68800 ymin,ymax (A): -22.29400 28.44100 zmin,zma (A): -10.54500 42.69600 x,y,z range (A): 44.68300 50.73500 53.24100 scale (grids/A): 2.005973 object centre (A): 10.34650 3.073501 16.07550 number of atom coordinates read : 2266 total number of charged atoms : 2127 net assigned charge : 1.500010 assigned positive charge : 336.9995 centred at (gu) : 95.29052 93.13105 90.55650 assigned negative charge : -335.4998 centred at (gu) : 95.13590 92.73405 89.88855 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 75613 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21136 grid for indexing accessible points = 1.400000 m= 26989 mr = 51359 m= 4527 mr = 19652 m= 345 mr = 2857 m= 8 mr = 155 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 33459 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 16795 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) : 0.6686575 object centre at (A) : 10.34650 3.073501 16.07550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3307937E-02 -6.1310842E-03 midg,1,midg; midg,igrid,midg 1.5532906E-02 7.6906629E-02 1,midg,midg; igrid,midg,midg -1.5803181E-02 -2.7121280E-04 gauss-seidel spectral radius is 0.9987408 estimated iterations to convergence 223 setup time was (sec) 0.9600000 now iterating at: 23:23:22 rms-change max change #iterations 4.364255 227.2099 at 10iterations 2.104898 77.19614 at 20iterations 1.010524 33.04036 at 30iterations 0.4893843 17.63647 at 40iterations 0.2360403 7.443462 at 50iterations 0.1139585 3.535131 at 60iterations 5.5155233E-02 1.724705 at 70iterations 2.6718765E-02 0.8273735 at 80iterations 1.2910020E-02 0.3915678 at 90iterations 6.2472643E-03 0.2161942 at 100iterations 3.0598086E-03 0.1018422 at 110iterations 1.5280187E-03 4.7632217E-02 at 120iterations finished qdiffx linear iterations at : 23:23:30 total time elapsed so far: 9.050000 # loops : 120 mean,max change (kT/e) : 1.5280187E-03 4.7632217E-02 energy calculations done at 9.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.230000 DelPhi exited at 23:23:31 9.228u 0.263s 0:10.10 93.8% 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 Sun Oct 9 2011 at 23:23:31 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2266 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: 3.008959 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): -11.99500 32.68800 ymin,ymax (A): -22.29400 28.44100 zmin,zma (A): -10.54500 42.69600 x,y,z range (A): 44.68300 50.73500 53.24100 scale (grids/A): 3.008959 object centre (A): 10.34650 3.073501 16.07550 number of atom coordinates read : 2266 total number of charged atoms : 2127 net assigned charge : 1.500010 assigned positive charge : 336.9995 centred at (gu) : 97.93553 94.69642 90.83482 assigned negative charge : -335.4998 centred at (gu) : 97.70387 94.10110 89.83286 start vw surface at 0.1500000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 174337 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21136 grid for indexing accessible points = 1.400000 m= 86983 mr = 124255 m= 31746 mr = 70653 m= 8194 mr = 25240 m= 1543 mr = 6164 m= 154 mr = 1135 m= 3 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.690000 number of dielectric boundary points 75407 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 17016 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) : 2.005973 object centre at (A) : 10.34650 3.073501 16.07550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8063828 -0.1775258 midg,1,midg; midg,igrid,midg 0.2206019 0.7512814 1,midg,midg; igrid,midg,midg -0.2266458 4.5113977E-02 gauss-seidel spectral radius is 0.9992906 estimated iterations to convergence 296 setup time was (sec) 2.010000 now iterating at: 23:23:33 rms-change max change #iterations 10.10857 432.4415 at 10iterations 5.966137 134.1737 at 20iterations 3.526177 71.11713 at 30iterations 2.071843 41.32496 at 40iterations 1.215930 24.40841 at 50iterations 0.7115247 15.56332 at 60iterations 0.4158398 7.954850 at 70iterations 0.2426890 4.293749 at 80iterations 0.1412277 2.710526 at 90iterations 8.2356825E-02 1.444696 at 100iterations 4.8048928E-02 0.9208088 at 110iterations 2.7925549E-02 0.4896626 at 120iterations 1.6255939E-02 0.3424435 at 130iterations 9.4836606E-03 0.1625600 at 140iterations 5.5236006E-03 0.1005135 at 150iterations 3.2267582E-03 6.1738968E-02 at 160iterations 1.8905725E-03 3.5345078E-02 at 170iterations 1.1196723E-03 2.2040486E-02 at 180iterations finished qdiffx linear iterations at : 23:23:47 total time elapsed so far: 15.42000 # loops : 180 mean,max change (kT/e) : 1.1196723E-03 2.2040486E-02 energy calculations done at 15.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.59000 DelPhi exited at 23:23:47 15.593u 0.294s 0:16.68 95.2% 0+0k 0+0io 0pf+0w