Sun Oct 9 09:01:03 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 09:01:03 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5655 !!! WARNING: HIR 701 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5269234 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): 15.45500 83.01700 ymin,ymax (A): 17.86400 84.17400 zmin,zma (A): 1.166000 68.00400 x,y,z range (A): 67.56200 66.31001 66.83800 scale (grids/A): 0.5269234 object centre (A): 49.23600 51.01900 34.58500 number of atom coordinates read : 5655 total number of charged atoms : 5488 net assigned charge : -4.485980 assigned positive charge : 850.2026 centred at (gu) : 90.54186 89.11463 90.60818 assigned negative charge : -854.6957 centred at (gu) : 90.49895 89.14838 90.69083 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 10070 nv = 96 ne = 84 npr = 113777 no. pairs analyzed = 113777 no. exposed pairs = 7295 no. arc points = 49410 no. surface atoms = 2413 nbur = 3242 mkacc time = 0.2000000 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 = 1.596000 m= 355 mr = 5223 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 40 time to turn everything in is 0.3700000 number of dielectric boundary points 5190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4985 ## 682 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 13445 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1509209E-10 -7.4734385E-10 midg,1,midg; midg,igrid,midg 9.7442013E-11 -2.6799576E-10 1,midg,midg; igrid,midg,midg -3.4142286E-10 1.5218365E-10 gauss-seidel spectral radius is 0.9816449 estimated iterations to convergence 61 setup time was (sec) 0.5700000 now iterating at: 09:01:04 rms-change max change #iterations 8.5244007E-02 12.73721 at 10iterations 5.5584912E-03 0.7152710 at 20iterations 5.4668490E-04 0.1153221 at 30iterations 1.3025294E-04 3.1524658E-02 at 40iterations 3.9889175E-05 9.2487335E-03 at 50iterations finished qdiffx linear iterations at : 09:01:06 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 3.9889175E-05 9.2487335E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 09:01:07 3.547u 0.145s 0:03.97 92.6% 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 09:01:07 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5655 !!! WARNING: HIR 701 has a net charge of 0.5140 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: 1.580770 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): 15.45500 83.01700 ymin,ymax (A): 17.86400 84.17400 zmin,zma (A): 1.166000 68.00400 x,y,z range (A): 67.56200 66.31001 66.83800 scale (grids/A): 1.580770 object centre (A): 49.23600 51.01900 34.58500 number of atom coordinates read : 5655 total number of charged atoms : 5488 net assigned charge : -4.485980 assigned positive charge : 850.2026 centred at (gu) : 91.62399 87.34207 91.82270 assigned negative charge : -854.6957 centred at (gu) : 91.49638 87.44482 92.07220 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 113047 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49410 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 34046 mr = 77629 m= 2974 mr = 22720 m= 49 mr = 1333 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 2139 time to turn everything in is 0.5200000 number of dielectric boundary points 48434 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 618 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 41672 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) : 0.5269234 object centre at (A) : 49.23600 51.01900 34.58500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1982405E-02 -4.7939382E-02 midg,1,midg; midg,igrid,midg -8.1759458E-03 -2.0156169E-02 1,midg,midg; igrid,midg,midg 3.4367922E-03 -7.8403158E-04 gauss-seidel spectral radius is 0.9983274 estimated iterations to convergence 194 setup time was (sec) 0.7400000 now iterating at: 09:01:08 rms-change max change #iterations 4.538731 172.4903 at 10iterations 1.954972 59.40236 at 20iterations 0.8450192 25.05553 at 30iterations 0.3656435 12.14437 at 40iterations 0.1577147 4.455755 at 50iterations 6.8348259E-02 2.076287 at 60iterations 2.9654045E-02 0.8108444 at 70iterations 1.2863885E-02 0.3806772 at 80iterations 5.5741537E-03 0.1655235 at 90iterations 2.4293577E-03 6.8971634E-02 at 100iterations 1.0692892E-03 3.1106472E-02 at 110iterations 4.7679429E-04 1.4778137E-02 at 120iterations finished qdiffx linear iterations at : 09:01:15 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 4.7679429E-04 1.4778137E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 09:01:15 8.005u 0.200s 0:08.51 96.3% 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 Sun Oct 9 2011 at 09:01:15 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5655 !!! WARNING: HIR 701 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.371156 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): 15.45500 83.01700 ymin,ymax (A): 17.86400 84.17400 zmin,zma (A): 1.166000 68.00400 x,y,z range (A): 67.56200 66.31001 66.83800 scale (grids/A): 2.371156 object centre (A): 49.23600 51.01900 34.58500 number of atom coordinates read : 5655 total number of charged atoms : 5488 net assigned charge : -4.485980 assigned positive charge : 850.2026 centred at (gu) : 92.43562 86.01273 92.73360 assigned negative charge : -854.6957 centred at (gu) : 92.24461 86.16715 93.10818 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 262744 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49410 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 120816 mr = 190276 m= 31708 mr = 94627 m= 4560 mr = 22949 m= 274 mr = 2874 m= 3 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 7004 time to turn everything in is 1.320000 number of dielectric boundary points 109288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 51 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 43794 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) : 1.580770 object centre at (A) : 49.23600 51.01900 34.58500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1877549 -1.083390 midg,1,midg; midg,igrid,midg -0.1263976 -0.3570229 1,midg,midg; igrid,midg,midg 0.2940996 0.1178665 gauss-seidel spectral radius is 0.9992550 estimated iterations to convergence 289 setup time was (sec) 1.560000 now iterating at: 09:01:17 rms-change max change #iterations 12.03992 281.5928 at 10iterations 7.180147 184.1331 at 20iterations 4.255660 81.39563 at 30iterations 2.507358 56.90989 at 40iterations 1.468882 27.51331 at 50iterations 0.8588757 16.96063 at 60iterations 0.5001035 8.882771 at 70iterations 0.2912953 5.960783 at 80iterations 0.1690597 2.941900 at 90iterations 9.8044142E-02 1.799646 at 100iterations 5.6744382E-02 0.9881229 at 110iterations 3.2777671E-02 0.5677843 at 120iterations 1.8964859E-02 0.3375382 at 130iterations 1.0952523E-02 0.2024632 at 140iterations 6.3261334E-03 0.1096885 at 150iterations 3.6470511E-03 6.5689087E-02 at 160iterations 2.1043322E-03 3.5087585E-02 at 170iterations 1.2177369E-03 1.9836426E-02 at 180iterations finished qdiffx linear iterations at : 09:01:29 total time elapsed so far: 13.36000 # loops : 180 mean,max change (kT/e) : 1.2177369E-03 1.9836426E-02 energy calculations done at 13.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.50000 DelPhi exited at 09:01:29 13.497u 0.211s 0:14.00 97.8% 0+0k 0+0io 0pf+0w