Mon Oct 10 14:13:29 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 Mon Oct 10 2011 at 14:13:29 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3365 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: 0.5110904 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): -19.17600 40.88900 ymin,ymax (A): -21.05300 34.37200 zmin,zma (A): -11.48000 58.17500 x,y,z range (A): 60.06500 55.42500 69.65500 scale (grids/A): 0.5110904 object centre (A): 10.85650 6.659499 23.34750 number of atom coordinates read : 3365 total number of charged atoms : 3218 net assigned charge : 4.500015 assigned positive charge : 521.5720 centred at (gu) : 89.01917 89.01801 91.19333 assigned negative charge : -517.0735 centred at (gu) : 88.97379 89.04779 91.13909 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5637 nv = 96 ne = 84 npr = 64264 no. pairs analyzed = 64264 no. exposed pairs = 4667 no. arc points = 33603 no. surface atoms = 1551 nbur = 1814 mkacc time = 0.1400000 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 = 1.680000 m= 189 mr = 2536 m= 0 mr = 3 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3407 ## 581 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7600 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8753890E-11 2.2889961E-10 midg,1,midg; midg,igrid,midg 1.5619689E-10 5.8757500E-12 1,midg,midg; igrid,midg,midg -3.1263183E-11 1.1631274E-10 gauss-seidel spectral radius is 0.9803296 estimated iterations to convergence 59 setup time was (sec) 0.5600000 now iterating at: 14:13:30 rms-change max change #iterations 5.5572011E-02 10.76912 at 10iterations 3.6521179E-03 0.7236900 at 20iterations 5.2034640E-04 0.1295967 at 30iterations 1.1678861E-04 3.0250549E-02 at 40iterations 2.7816854E-05 7.1334839E-03 at 50iterations finished qdiffx linear iterations at : 14:13:32 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 2.7816854E-05 7.1334839E-03 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 14:13:33 3.204u 0.182s 0:03.85 87.7% 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 14:13:33 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3365 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: 1.533271 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): -19.17600 40.88900 ymin,ymax (A): -21.05300 34.37200 zmin,zma (A): -11.48000 58.17500 x,y,z range (A): 60.06500 55.42500 69.65500 scale (grids/A): 1.533271 object centre (A): 10.85650 6.659499 23.34750 number of atom coordinates read : 3365 total number of charged atoms : 3218 net assigned charge : 4.500015 assigned positive charge : 521.5720 centred at (gu) : 87.05620 87.05287 93.57914 assigned negative charge : -517.0735 centred at (gu) : 86.92105 87.14302 93.41660 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 62632 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33603 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 15958 mr = 39214 m= 1222 mr = 9588 m= 24 mr = 424 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 459 time to turn everything in is 0.4500000 number of dielectric boundary points 30610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 577 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 24237 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) : 0.5110904 object centre at (A) : 10.85650 6.659499 23.34750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8706463E-03 7.7554425E-03 midg,1,midg; midg,igrid,midg 3.9155507E-03 -1.8522254E-03 1,midg,midg; igrid,midg,midg -2.4596970E-03 1.4997268E-03 gauss-seidel spectral radius is 0.9979783 estimated iterations to convergence 177 setup time was (sec) 0.7200000 now iterating at: 14:13:34 rms-change max change #iterations 3.136902 148.9355 at 10iterations 1.241893 60.21275 at 20iterations 0.4928098 17.87335 at 30iterations 0.1954736 8.599463 at 40iterations 7.7469036E-02 2.878046 at 50iterations 3.0866595E-02 1.206543 at 60iterations 1.2406341E-02 0.4589119 at 70iterations 5.0243465E-03 0.2208138 at 80iterations 2.0854708E-03 0.1033478 at 90iterations 9.1175642E-04 4.3643951E-02 at 100iterations 4.2975589E-04 2.0772934E-02 at 110iterations 2.2106897E-04 1.1508942E-02 at 120iterations finished qdiffx linear iterations at : 14:13:40 total time elapsed so far: 7.180000 # loops : 120 mean,max change (kT/e) : 2.2106897E-04 1.1508942E-02 energy calculations done at 7.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.360000 DelPhi exited at 14:13:41 7.359u 0.223s 0:08.04 94.1% 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 14:13:41 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3365 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: 2.299907 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): -19.17600 40.88900 ymin,ymax (A): -21.05300 34.37200 zmin,zma (A): -11.48000 58.17500 x,y,z range (A): 60.06500 55.42500 69.65500 scale (grids/A): 2.299907 object centre (A): 10.85650 6.659499 23.34750 number of atom coordinates read : 3365 total number of charged atoms : 3218 net assigned charge : 4.500015 assigned positive charge : 521.5720 centred at (gu) : 85.58395 85.57899 95.36844 assigned negative charge : -517.0735 centred at (gu) : 85.38142 85.71429 95.12474 start vw surface at 0.1700000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 145535 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33603 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 58419 mr = 97272 m= 13172 mr = 42972 m= 1696 mr = 8707 m= 93 mr = 919 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.5699999 no. cavity mid-points inaccessible to solvent = 1381 time to turn everything in is 1.060000 number of dielectric boundary points 69018 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 25670 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) : 1.533271 object centre at (A) : 10.85650 6.659499 23.34750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2243839 0.1519667 midg,1,midg; midg,igrid,midg 5.3649105E-02 -2.7520921E-02 1,midg,midg; igrid,midg,midg -3.3511359E-03 5.2187177E-03 gauss-seidel spectral radius is 0.9990913 estimated iterations to convergence 262 setup time was (sec) 1.380000 now iterating at: 14:13:43 rms-change max change #iterations 8.694606 303.5887 at 10iterations 4.894944 147.2346 at 20iterations 2.730800 71.20082 at 30iterations 1.513627 37.53128 at 40iterations 0.8336197 20.36386 at 50iterations 0.4580250 11.31560 at 60iterations 0.2508606 5.719639 at 70iterations 0.1372001 3.134235 at 80iterations 7.4580498E-02 1.819063 at 90iterations 4.0662587E-02 0.9603176 at 100iterations 2.2149362E-02 0.4831352 at 110iterations 1.2038032E-02 0.2904625 at 120iterations 6.5579759E-03 0.1546936 at 130iterations 3.5830408E-03 7.8529358E-02 at 140iterations 1.9686166E-03 4.3994904E-02 at 150iterations 1.0920415E-03 2.6000977E-02 at 160iterations 6.1412301E-04 1.5155792E-02 at 170iterations 3.5490352E-04 8.9721680E-03 at 180iterations finished qdiffx linear iterations at : 14:13:53 total time elapsed so far: 11.76000 # loops : 180 mean,max change (kT/e) : 3.5490352E-04 8.9721680E-03 energy calculations done at 11.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.94000 DelPhi exited at 14:13:54 11.944u 0.200s 0:12.70 95.5% 0+0k 0+0io 0pf+0w