Sun Oct 9 13:12:40 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 Sun Oct 9 2011 at 13:12:40 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 = 2352 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: 0.7069804 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): -18.80800 30.23900 ymin,ymax (A): -20.43700 29.91800 zmin,zma (A): 4.502000 48.94000 x,y,z range (A): 49.04700 50.35500 44.43800 scale (grids/A): 0.7069804 object centre (A): 5.715500 4.740500 26.72100 number of atom coordinates read : 2352 total number of charged atoms : 2211 net assigned charge : 2.500011 assigned positive charge : 356.2352 centred at (gu) : 90.83617 90.22002 90.05915 assigned negative charge : -353.7356 centred at (gu) : 90.93977 90.39083 90.14735 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8104 nv = 96 ne = 84 npr = 47040 no. pairs analyzed = 47040 no. exposed pairs = 3049 no. arc points = 21041 no. surface atoms = 1020 nbur = 1332 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 539 mr = 4547 m= 2 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 7.9999991E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 4005 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1865 ## 175 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8838 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9479718E-08 -2.7880251E-08 midg,1,midg; midg,igrid,midg 1.1005620E-07 -7.7976480E-08 1,midg,midg; igrid,midg,midg 6.6799956E-08 -4.3131607E-08 gauss-seidel spectral radius is 0.9896026 estimated iterations to convergence 80 setup time was (sec) 0.3800000 now iterating at: 13:12:40 rms-change max change #iterations 0.2150375 29.51048 at 10iterations 2.6367052E-02 3.325401 at 20iterations 3.8057887E-03 0.5082436 at 30iterations 8.0380507E-04 0.1276207 at 40iterations 2.5488611E-04 3.8646698E-02 at 50iterations finished qdiffx linear iterations at : 13:12:43 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 2.5488611E-04 3.8646698E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 13:12:44 3.399u 0.190s 0:03.93 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 13:12:44 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 = 2352 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: 2.120941 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): -18.80800 30.23900 ymin,ymax (A): -20.43700 29.91800 zmin,zma (A): 4.502000 48.94000 x,y,z range (A): 49.04700 50.35500 44.43800 scale (grids/A): 2.120941 object centre (A): 5.715500 4.740500 26.72100 number of atom coordinates read : 2352 total number of charged atoms : 2211 net assigned charge : 2.500011 assigned positive charge : 356.2352 centred at (gu) : 92.50829 90.65981 90.17699 assigned negative charge : -353.7356 centred at (gu) : 92.81921 91.17226 90.44168 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 85921 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21041 grid for indexing accessible points = 1.400000 m= 33522 mr = 60154 m= 6229 mr = 24905 m= 621 mr = 4109 m= 16 mr = 313 m= 0 mr = 1 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 36827 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 82 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 17540 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) : 0.7069804 object centre at (A) : 5.715500 4.740500 26.72100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5993184E-02 8.9522935E-03 midg,1,midg; midg,igrid,midg -1.3116988E-02 -0.1163498 1,midg,midg; igrid,midg,midg 1.1863209E-03 -3.6706009E-03 gauss-seidel spectral radius is 0.9988654 estimated iterations to convergence 235 setup time was (sec) 0.6600000 now iterating at: 13:12:44 rms-change max change #iterations 4.946931 201.6850 at 10iterations 2.469985 74.15666 at 20iterations 1.236025 35.99062 at 30iterations 0.6189365 17.97148 at 40iterations 0.3104334 9.293493 at 50iterations 0.1555870 4.494797 at 60iterations 7.8067325E-02 2.145092 at 70iterations 3.9266910E-02 1.063087 at 80iterations 1.9825762E-02 0.6081777 at 90iterations 1.0094762E-02 0.2759209 at 100iterations 5.2042906E-03 0.1539345 at 110iterations 2.7621416E-03 8.6494446E-02 at 120iterations finished qdiffx linear iterations at : 13:12:52 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 2.7621416E-03 8.6494446E-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) 8.010000 DelPhi exited at 13:12:52 8.013u 0.190s 0:08.50 96.4% 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 Sun Oct 9 2011 at 13:12:52 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 = 2352 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: 3.181412 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): -18.80800 30.23900 ymin,ymax (A): -20.43700 29.91800 zmin,zma (A): 4.502000 48.94000 x,y,z range (A): 49.04700 50.35500 44.43800 scale (grids/A): 3.181412 object centre (A): 5.715500 4.740500 26.72100 number of atom coordinates read : 2352 total number of charged atoms : 2211 net assigned charge : 2.500011 assigned positive charge : 356.2352 centred at (gu) : 93.76249 90.98961 90.26534 assigned negative charge : -353.7356 centred at (gu) : 94.22866 91.75840 90.66248 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 198106 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21041 grid for indexing accessible points = 1.400000 m= 105076 mr = 144973 m= 41152 mr = 86337 m= 11715 mr = 33492 m= 2488 mr = 9022 m= 269 mr = 1772 m= 12 mr = 169 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.320000 number of dielectric boundary points 83053 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 17687 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) : 2.120941 object centre at (A) : 5.715500 4.740500 26.72100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5398490 -1.7302725E-02 midg,1,midg; midg,igrid,midg -0.5116442 -1.308849 1,midg,midg; igrid,midg,midg -7.5895086E-02 -6.1234444E-02 gauss-seidel spectral radius is 0.9993091 estimated iterations to convergence 300 setup time was (sec) 1.550000 now iterating at: 13:12:54 rms-change max change #iterations 11.08340 397.8256 at 10iterations 6.647243 127.6880 at 20iterations 3.964522 76.98309 at 30iterations 2.364646 45.48738 at 40iterations 1.402287 26.86042 at 50iterations 0.8300621 13.94024 at 60iterations 0.4912041 9.582124 at 70iterations 0.2904108 4.766791 at 80iterations 0.1716451 2.932325 at 90iterations 0.1010800 1.828623 at 100iterations 5.9756752E-02 1.076280 at 110iterations 3.5314918E-02 0.6943347 at 120iterations 2.1091849E-02 0.3846283 at 130iterations 1.2734113E-02 0.2086945 at 140iterations 7.8842491E-03 0.1449165 at 150iterations 5.0672912E-03 0.1041222 at 160iterations 3.4518384E-03 7.2946548E-02 at 170iterations 2.5093015E-03 5.2101135E-02 at 180iterations finished qdiffx linear iterations at : 13:13:05 total time elapsed so far: 13.05000 # loops : 180 mean,max change (kT/e) : 2.5093015E-03 5.2101135E-02 energy calculations done at 13.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.19000 DelPhi exited at 13:13:06 13.189u 0.207s 0:13.67 97.8% 0+0k 0+0io 0pf+0w