Sun Oct 9 06:31:44 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 06:31:44 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 !!! WARNING: ASP 186 has a net charge of -2.0000 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: 0.6717361 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): 1.406000 43.96100 ymin,ymax (A): -9.302000 37.47400 zmin,zma (A): -24.76700 28.23000 x,y,z range (A): 42.55500 46.77600 52.99700 scale (grids/A): 0.6717361 object centre (A): 22.68350 14.08600 1.731500 number of atom coordinates read : 1946 total number of charged atoms : 1807 net assigned charge : 0.5000135 assigned positive charge : 289.9030 centred at (gu) : 90.09505 89.40509 88.48833 assigned negative charge : -289.4032 centred at (gu) : 89.92166 89.26710 88.38336 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5904 nv = 96 ne = 84 npr = 40081 no. pairs analyzed = 40081 no. exposed pairs = 2462 no. arc points = 17538 no. surface atoms = 828 nbur = 1118 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 392 mr = 3205 m= 0 mr = 71 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2400000 number of dielectric boundary points 3020 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1632 ## 136 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6776 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5753229E-08 1.6709455E-08 midg,1,midg; midg,igrid,midg -2.8768008E-08 2.5793527E-08 1,midg,midg; igrid,midg,midg -3.1960621E-08 3.6675058E-08 gauss-seidel spectral radius is 0.9884532 estimated iterations to convergence 76 setup time was (sec) 0.4700000 now iterating at: 06:31:44 rms-change max change #iterations 0.1534099 31.27704 at 10iterations 1.6849456E-02 2.325874 at 20iterations 1.8313694E-03 0.2859459 at 30iterations 2.0297969E-04 3.3973694E-02 at 40iterations 2.2373679E-05 3.7422180E-03 at 50iterations finished qdiffx linear iterations at : 06:31:47 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 2.2373679E-05 3.7422180E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 06:31:48 3.344u 0.209s 0:03.83 92.4% 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 06:31:48 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 !!! WARNING: ASP 186 has a net charge of -2.0000 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: 2.015208 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): 1.406000 43.96100 ymin,ymax (A): -9.302000 37.47400 zmin,zma (A): -24.76700 28.23000 x,y,z range (A): 42.55500 46.77600 52.99700 scale (grids/A): 2.015208 object centre (A): 22.68350 14.08600 1.731500 number of atom coordinates read : 1946 total number of charged atoms : 1807 net assigned charge : 0.5000135 assigned positive charge : 289.9030 centred at (gu) : 90.28514 88.21525 85.46511 assigned negative charge : -289.4032 centred at (gu) : 89.76516 87.80154 85.15025 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 62635 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17538 grid for indexing accessible points = 1.400000 m= 23917 mr = 42538 m= 4388 mr = 17942 m= 344 mr = 2998 m= 8 mr = 144 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 404 time to turn everything in is 0.4600000 number of dielectric boundary points 27670 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 75 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 14313 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) : 0.6717361 object centre at (A) : 22.68350 14.08600 1.731500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8884112E-02 3.4668554E-02 midg,1,midg; midg,igrid,midg -2.1795515E-02 6.7611774E-03 1,midg,midg; igrid,midg,midg -2.5241556E-02 2.5174271E-02 gauss-seidel spectral radius is 0.9987108 estimated iterations to convergence 221 setup time was (sec) 0.7500000 now iterating at: 06:31:49 rms-change max change #iterations 4.050078 215.2282 at 10iterations 1.929081 73.05866 at 20iterations 0.9199964 31.97732 at 30iterations 0.4402076 16.01027 at 40iterations 0.2098940 7.718258 at 50iterations 0.1007977 3.652065 at 60iterations 4.8041910E-02 1.625813 at 70iterations 2.2960888E-02 0.7549040 at 80iterations 1.0951831E-02 0.3864565 at 90iterations 5.2383812E-03 0.1950760 at 100iterations 2.5060214E-03 8.3728790E-02 at 110iterations 1.1996179E-03 4.2437315E-02 at 120iterations finished qdiffx linear iterations at : 06:31:55 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 1.1996179E-03 4.2437315E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 06:31:56 7.637u 0.243s 0:08.18 96.2% 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 06:31:56 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 !!! WARNING: ASP 186 has a net charge of -2.0000 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: 3.022813 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): 1.406000 43.96100 ymin,ymax (A): -9.302000 37.47400 zmin,zma (A): -24.76700 28.23000 x,y,z range (A): 42.55500 46.77600 52.99700 scale (grids/A): 3.022813 object centre (A): 22.68350 14.08600 1.731500 number of atom coordinates read : 1946 total number of charged atoms : 1807 net assigned charge : 0.5000135 assigned positive charge : 289.9030 centred at (gu) : 90.42764 87.32272 83.19766 assigned negative charge : -289.4032 centred at (gu) : 89.64792 86.70230 82.72533 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 144725 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17538 grid for indexing accessible points = 1.400000 m= 74780 mr = 102964 m= 29767 mr = 61510 m= 8301 mr = 24542 m= 1422 mr = 6489 m= 107 mr = 998 m= 3 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 1229 time to turn everything in is 1.190000 number of dielectric boundary points 62562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 14456 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) : 2.015208 object centre at (A) : 22.68350 14.08600 1.731500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5921867 0.9586322 midg,1,midg; midg,igrid,midg -0.1454087 7.0258565E-02 1,midg,midg; igrid,midg,midg -0.2056186 0.2309429 gauss-seidel spectral radius is 0.9992658 estimated iterations to convergence 291 setup time was (sec) 1.500000 now iterating at: 06:31:58 rms-change max change #iterations 9.217337 480.4087 at 10iterations 5.325310 125.7299 at 20iterations 3.077848 72.93645 at 30iterations 1.776954 35.75343 at 40iterations 1.022648 24.91764 at 50iterations 0.5900571 10.95376 at 60iterations 0.3389154 6.225406 at 70iterations 0.1950586 4.045560 at 80iterations 0.1118173 2.208466 at 90iterations 6.4359210E-02 1.217350 at 100iterations 3.6944561E-02 0.6912766 at 110iterations 2.1210365E-02 0.4295006 at 120iterations 1.2227838E-02 0.2216530 at 130iterations 7.0303404E-03 0.1520510 at 140iterations 4.0306356E-03 7.4420691E-02 at 150iterations 2.3237297E-03 4.4328690E-02 at 160iterations 1.3352481E-03 2.4841309E-02 at 170iterations 7.6662429E-04 1.6109467E-02 at 180iterations finished qdiffx linear iterations at : 06:32:08 total time elapsed so far: 12.18000 # loops : 180 mean,max change (kT/e) : 7.6662429E-04 1.6109467E-02 energy calculations done at 12.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.34000 DelPhi exited at 06:32:09 12.345u 0.262s 0:12.93 97.4% 0+0k 0+0io 0pf+0w