Sat Oct 8 11:43:10 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 8 2011 at 11:43:10 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 = 5310 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.2200000 grid size : 179 scale,in grids/A, set to be: 0.5401223 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): 7.323000 72.97100 ymin,ymax (A): 4.596000 69.14200 zmin,zma (A): 9.408000 75.31900 x,y,z range (A): 65.64800 64.54600 65.91100 scale (grids/A): 0.5401223 object centre (A): 40.14700 36.86900 42.36350 number of atom coordinates read : 5310 total number of charged atoms : 5140 net assigned charge : 0.5000382 assigned positive charge : 805.4238 centred at (gu) : 90.20129 90.22699 91.24219 assigned negative charge : -804.9294 centred at (gu) : 90.13743 90.21441 91.28442 start vw surface at 0.3000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 9548 nv = 96 ne = 84 npr = 110679 no. pairs analyzed = 110679 no. exposed pairs = 6288 no. arc points = 42470 no. surface atoms = 2103 nbur = 3207 mkacc time = 0.3100000 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= 378 mr = 5232 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 4675 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4330 ## 599 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 12937 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1683647E-10 -5.2319360E-10 midg,1,midg; midg,igrid,midg -8.7383698E-11 1.5847113E-10 1,midg,midg; igrid,midg,midg -5.6171107E-10 6.7212697E-10 gauss-seidel spectral radius is 0.9824923 estimated iterations to convergence 62 setup time was (sec) 0.9500000 now iterating at: 11:43:11 rms-change max change #iterations 9.3588941E-02 13.52385 at 10iterations 7.6518035E-03 1.324486 at 20iterations 1.2650409E-03 0.2976761 at 30iterations 3.2860014E-04 7.4470520E-02 at 40iterations 9.3698844E-05 1.9577026E-02 at 50iterations finished qdiffx linear iterations at : 11:43:14 total time elapsed so far: 4.110000 # loops : 50 mean,max change (kT/e) : 9.3698844E-05 1.9577026E-02 energy calculations done at 4.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.350000 DelPhi exited at 11:43:15 4.351u 0.179s 0:04.82 93.7% 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 Sat Oct 8 2011 at 11:43:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5310 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 1.620367 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): 7.323000 72.97100 ymin,ymax (A): 4.596000 69.14200 zmin,zma (A): 9.408000 75.31900 x,y,z range (A): 65.64800 64.54600 65.91100 scale (grids/A): 1.620367 object centre (A): 40.14700 36.86900 42.36350 number of atom coordinates read : 5310 total number of charged atoms : 5140 net assigned charge : 0.5000382 assigned positive charge : 805.4238 centred at (gu) : 90.60233 90.67922 93.72527 assigned negative charge : -804.9294 centred at (gu) : 90.41180 90.64292 93.85294 start vw surface at 0.2600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 108492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42470 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 33656 mr = 77156 m= 3495 mr = 23205 m= 83 mr = 1715 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 1493 time to turn everything in is 0.9400000 number of dielectric boundary points 43644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 508 ## 4 charges are in solution ## iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 39247 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) : 0.5401223 object centre at (A) : 40.14700 36.86900 42.36350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4440605E-02 -1.3869869E-03 midg,1,midg; midg,igrid,midg -7.7292537E-03 1.8340966E-02 1,midg,midg; igrid,midg,midg -1.1475286E-02 1.2029389E-02 gauss-seidel spectral radius is 0.9983720 estimated iterations to convergence 197 setup time was (sec) 1.300000 now iterating at: 11:43:16 rms-change max change #iterations 4.597138 154.5029 at 10iterations 2.002051 57.98907 at 20iterations 0.8750347 26.09300 at 30iterations 0.3830047 12.10992 at 40iterations 0.1681890 5.032932 at 50iterations 7.3567376E-02 2.130620 at 60iterations 3.2314129E-02 0.9068146 at 70iterations 1.4246467E-02 0.4929924 at 80iterations 6.3320687E-03 0.1765790 at 90iterations 2.8481192E-03 9.2269897E-02 at 100iterations 1.3111248E-03 4.3624878E-02 at 110iterations 6.3317770E-04 2.3155212E-02 at 120iterations finished qdiffx linear iterations at : 11:43:24 total time elapsed so far: 9.050000 # loops : 120 mean,max change (kT/e) : 6.3317770E-04 2.3155212E-02 energy calculations done at 9.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.280000 DelPhi exited at 11:43:24 9.282u 0.177s 0:09.73 97.1% 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 8 2011 at 11:43:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5310 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.430550 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): 7.323000 72.97100 ymin,ymax (A): 4.596000 69.14200 zmin,zma (A): 9.408000 75.31900 x,y,z range (A): 65.64800 64.54600 65.91100 scale (grids/A): 2.430550 object centre (A): 40.14700 36.86900 42.36350 number of atom coordinates read : 5310 total number of charged atoms : 5140 net assigned charge : 0.5000382 assigned positive charge : 805.4238 centred at (gu) : 90.90318 91.01848 95.58742 assigned negative charge : -804.9294 centred at (gu) : 90.61768 90.96445 95.77930 start vw surface at 0.2900000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 253494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42470 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 117139 mr = 189373 m= 33479 mr = 93279 m= 5287 mr = 25151 m= 312 mr = 3400 m= 3 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 1.400000 no. cavity mid-points inaccessible to solvent = 5093 time to turn everything in is 2.360000 number of dielectric boundary points 98403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 2.540000 number of grid points assigned charge 41069 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) : 1.620367 object centre at (A) : 40.14700 36.86900 42.36350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2017098 -0.3336295 midg,1,midg; midg,igrid,midg -0.1313803 0.2000871 1,midg,midg; igrid,midg,midg -0.2505403 4.8016001E-02 gauss-seidel spectral radius is 0.9992446 estimated iterations to convergence 287 setup time was (sec) 2.740000 now iterating at: 11:43:27 rms-change max change #iterations 12.07938 309.6620 at 10iterations 7.194232 161.7166 at 20iterations 4.253387 92.63313 at 30iterations 2.502839 48.19698 at 40iterations 1.464612 31.93414 at 50iterations 0.8552907 19.18444 at 60iterations 0.4972687 9.381771 at 70iterations 0.2886961 5.059183 at 80iterations 0.1670232 3.149223 at 90iterations 9.6640833E-02 1.676506 at 100iterations 5.5959631E-02 1.108360 at 110iterations 3.2320753E-02 0.6659837 at 120iterations 1.8693136E-02 0.3736763 at 130iterations 1.0789499E-02 0.1925077 at 140iterations 6.2640319E-03 0.1131439 at 150iterations 3.6353092E-03 7.5435638E-02 at 160iterations 2.1226429E-03 4.0708542E-02 at 170iterations 1.2538112E-03 2.3242950E-02 at 180iterations finished qdiffx linear iterations at : 11:43:40 total time elapsed so far: 15.34000 # loops : 180 mean,max change (kT/e) : 1.2538112E-03 2.3242950E-02 energy calculations done at 15.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.58000 DelPhi exited at 11:43:40 15.578u 0.182s 0:16.03 98.2% 0+0k 0+0io 0pf+0w