Sat Oct 15 14:04:55 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 14:04:57 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 = 4761 !!! 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: 0.5133826 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): -17.97500 36.94900 ymin,ymax (A): -30.84100 34.10800 zmin,zma (A): -3.917000 65.42700 x,y,z range (A): 54.92400 64.94901 69.34400 scale (grids/A): 0.5133826 object centre (A): 9.487000 1.633501 30.75500 number of atom coordinates read : 4761 total number of charged atoms : 4515 net assigned charge : 7.800033 assigned positive charge : 715.0155 centred at (gu) : 90.15199 90.47011 88.34055 assigned negative charge : -707.2200 centred at (gu) : 90.04047 90.52589 88.30140 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8007 nv = 96 ne = 84 npr = 95977 no. pairs analyzed = 95977 no. exposed pairs = 6103 no. arc points = 42260 no. surface atoms = 2045 nbur = 2716 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= 292 mr = 4137 m= 0 mr = 3 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4159 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4057 ## 576 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 10552 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8126679E-11 1.5627977E-10 midg,1,midg; midg,igrid,midg 2.5389743E-10 -3.9866725E-11 1,midg,midg; igrid,midg,midg -1.9058811E-10 4.6215956E-10 gauss-seidel spectral radius is 0.9805980 estimated iterations to convergence 59 setup time was (sec) 0.5300000 now iterating at: 14:04:58 rms-change max change #iterations 6.9704935E-02 10.17169 at 10iterations 4.2641093E-03 0.6680756 at 20iterations 5.6200335E-04 7.9795361E-02 at 30iterations 2.0698318E-04 3.0768961E-02 at 40iterations 8.4425454E-05 1.2431860E-02 at 50iterations finished qdiffx linear iterations at : 14:05:04 total time elapsed so far: 3.620000 # loops : 50 mean,max change (kT/e) : 8.4425454E-05 1.2431860E-02 energy calculations done at 3.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.780000 DelPhi exited at 14:05:05 3.781u 0.250s 0:08.31 48.4% 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 14:05:06 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4761 !!! 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: 1.540148 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): -17.97500 36.94900 ymin,ymax (A): -30.84100 34.10800 zmin,zma (A): -3.917000 65.42700 x,y,z range (A): 54.92400 64.94901 69.34400 scale (grids/A): 1.540148 object centre (A): 9.487000 1.633501 30.75500 number of atom coordinates read : 4761 total number of charged atoms : 4515 net assigned charge : 7.800033 assigned positive charge : 715.0155 centred at (gu) : 90.45461 91.40918 85.02018 assigned negative charge : -707.2200 centred at (gu) : 90.12141 91.57764 84.90395 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 90636 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42260 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26209 mr = 62129 m= 2317 mr = 17283 m= 51 mr = 945 m= 0 mr = 7 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 38849 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 544 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 33996 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) : 0.5133826 object centre at (A) : 9.487000 1.633501 30.75500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5456270E-03 2.1407012E-02 midg,1,midg; midg,igrid,midg 9.3706055E-03 -1.2382773E-02 1,midg,midg; igrid,midg,midg -1.7447985E-03 1.1737998E-02 gauss-seidel spectral radius is 0.9981382 estimated iterations to convergence 184 setup time was (sec) 0.7300000 now iterating at: 14:05:08 rms-change max change #iterations 3.827706 171.4372 at 10iterations 1.575897 55.24325 at 20iterations 0.6498677 19.91374 at 30iterations 0.2689946 8.460709 at 40iterations 0.1110674 3.715155 at 50iterations 4.6061769E-02 1.361495 at 60iterations 1.9020684E-02 0.7663383 at 70iterations 7.9419063E-03 0.2659569 at 80iterations 3.3293436E-03 0.1089926 at 90iterations 1.4285629E-03 4.1701317E-02 at 100iterations 6.5633893E-04 2.3803711E-02 at 110iterations 3.4122696E-04 1.1680603E-02 at 120iterations finished qdiffx linear iterations at : 14:05:23 total time elapsed so far: 8.760000 # loops : 120 mean,max change (kT/e) : 3.4122696E-04 1.1680603E-02 energy calculations done at 8.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.890000 DelPhi exited at 14:05:24 8.891u 0.262s 0:17.88 51.1% 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 Sat Oct 15 2011 at 14:05:24 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 = 4761 !!! 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: 2.310221 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): -17.97500 36.94900 ymin,ymax (A): -30.84100 34.10800 zmin,zma (A): -3.917000 65.42700 x,y,z range (A): 54.92400 64.94901 69.34400 scale (grids/A): 2.310221 object centre (A): 9.487000 1.633501 30.75500 number of atom coordinates read : 4761 total number of charged atoms : 4515 net assigned charge : 7.800033 assigned positive charge : 715.0155 centred at (gu) : 90.68159 92.11324 82.52986 assigned negative charge : -707.2200 centred at (gu) : 90.18195 92.36629 82.35587 start vw surface at 0.1200000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 211319 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42260 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 94010 mr = 152874 m= 23489 mr = 73145 m= 3254 mr = 16471 m= 194 mr = 1936 m= 2 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.110000 number of dielectric boundary points 87775 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 36045 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) : 1.540148 object centre at (A) : 9.487000 1.633501 30.75500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1327833 0.4812403 midg,1,midg; midg,igrid,midg 0.1986033 -0.2717761 1,midg,midg; igrid,midg,midg -2.2085058E-02 0.1627823 gauss-seidel spectral radius is 0.9991744 estimated iterations to convergence 275 setup time was (sec) 1.380000 now iterating at: 14:05:26 rms-change max change #iterations 10.36461 340.1484 at 10iterations 5.978652 131.1504 at 20iterations 3.424394 77.35195 at 30iterations 1.947393 39.78776 at 40iterations 1.102082 27.23034 at 50iterations 0.6219658 13.64623 at 60iterations 0.3502186 7.147131 at 70iterations 0.1971475 4.646451 at 80iterations 0.1104838 2.412498 at 90iterations 6.1812371E-02 1.310651 at 100iterations 3.4617923E-02 0.8234377 at 110iterations 1.9395690E-02 0.4112759 at 120iterations 1.0828841E-02 0.2001786 at 130iterations 6.0798735E-03 0.1152973 at 140iterations 3.4091398E-03 6.5848351E-02 at 150iterations 1.9205253E-03 3.6743164E-02 at 160iterations 1.0944239E-03 2.2064209E-02 at 170iterations 6.3492544E-04 1.3208389E-02 at 180iterations finished qdiffx linear iterations at : 14:05:46 total time elapsed so far: 13.82000 # loops : 180 mean,max change (kT/e) : 6.3492544E-04 1.3208389E-02 energy calculations done at 13.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.95000 DelPhi exited at 14:05:46 13.955u 0.286s 0:22.62 62.9% 0+0k 0+0io 0pf+0w