Mon Oct 10 17:12:59 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 Mon Oct 10 2011 at 17:12:59 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 = 3154 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: 0.6108861 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): -9.297999 47.97800 ymin,ymax (A): -9.015000 43.76000 zmin,zma (A): -3.853000 54.42300 x,y,z range (A): 57.27600 52.77500 58.27600 scale (grids/A): 0.6108861 object centre (A): 19.34000 17.37250 25.28500 number of atom coordinates read : 3154 total number of charged atoms : 3012 net assigned charge : -2.999964 assigned positive charge : 474.0156 centred at (gu) : 89.68639 88.53281 89.09722 assigned negative charge : -477.0169 centred at (gu) : 89.64675 88.43633 88.96669 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7893 nv = 96 ne = 84 npr = 63667 no. pairs analyzed = 63667 no. exposed pairs = 4047 no. arc points = 28169 no. surface atoms = 1371 nbur = 1783 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 354 mr = 4223 m= 3 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.3800000 number of dielectric boundary points 4006 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2874 ## 286 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9815 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2101809E-08 5.1924705E-09 midg,1,midg; midg,igrid,midg -1.0723932E-08 3.0832068E-09 1,midg,midg; igrid,midg,midg -4.3903867E-09 7.7583534E-10 gauss-seidel spectral radius is 0.9861773 estimated iterations to convergence 70 setup time was (sec) 0.6100000 now iterating at: 17:13:00 rms-change max change #iterations 0.1309715 18.55579 at 10iterations 1.1620677E-02 1.601936 at 20iterations 1.0520001E-03 0.1625786 at 30iterations 9.3624556E-05 1.4388233E-02 at 40iterations 9.0280482E-06 1.2249947E-03 at 50iterations finished qdiffx linear iterations at : 17:13:03 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 9.0280482E-06 1.2249947E-03 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 17:13:03 3.709u 0.202s 0:04.35 89.6% 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 Mon Oct 10 2011 at 17:13:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3154 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: 1.832658 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): -9.297999 47.97800 ymin,ymax (A): -9.015000 43.76000 zmin,zma (A): -3.853000 54.42300 x,y,z range (A): 57.27600 52.77500 58.27600 scale (grids/A): 1.832658 object centre (A): 19.34000 17.37250 25.28500 number of atom coordinates read : 3154 total number of charged atoms : 3012 net assigned charge : -2.999964 assigned positive charge : 474.0156 centred at (gu) : 89.05846 85.59731 87.29049 assigned negative charge : -477.0169 centred at (gu) : 88.93991 85.30854 86.89991 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 85429 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28169 grid for indexing accessible points = 1.400000 m= 28502 mr = 58588 m= 3769 mr = 20124 m= 180 mr = 2136 m= 3 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1015 time to turn everything in is 0.6400000 number of dielectric boundary points 36978 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 207 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 23601 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) : 0.6108861 object centre at (A) : 19.34000 17.37250 25.28500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0461649E-03 1.8298285E-02 midg,1,midg; midg,igrid,midg -3.5195623E-02 4.2212647E-03 1,midg,midg; igrid,midg,midg -4.3338183E-02 2.0629231E-02 gauss-seidel spectral radius is 0.9985815 estimated iterations to convergence 210 setup time was (sec) 0.9500000 now iterating at: 17:13:04 rms-change max change #iterations 4.387297 167.5789 at 10iterations 2.026114 70.85284 at 20iterations 0.9308363 32.41330 at 30iterations 0.4314524 12.83774 at 40iterations 0.1979117 6.079256 at 50iterations 9.1376714E-02 2.726589 at 60iterations 4.2161684E-02 1.304368 at 70iterations 1.9416284E-02 0.6124228 at 80iterations 9.0014637E-03 0.2764337 at 90iterations 4.1372157E-03 0.1311693 at 100iterations 1.9125609E-03 5.8399081E-02 at 110iterations 8.8159769E-04 2.4736404E-02 at 120iterations finished qdiffx linear iterations at : 17:13:12 total time elapsed so far: 8.200000 # loops : 120 mean,max change (kT/e) : 8.8159769E-04 2.4736404E-02 energy calculations done at 8.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.380000 DelPhi exited at 17:13:12 8.380u 0.265s 0:09.03 95.6% 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 Mon Oct 10 2011 at 17:13:12 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 = 3154 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: 2.748987 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): -9.297999 47.97800 ymin,ymax (A): -9.015000 43.76000 zmin,zma (A): -3.853000 54.42300 x,y,z range (A): 57.27600 52.77500 58.27600 scale (grids/A): 2.748987 object centre (A): 19.34000 17.37250 25.28500 number of atom coordinates read : 3154 total number of charged atoms : 3012 net assigned charge : -2.999964 assigned positive charge : 474.0156 centred at (gu) : 88.58750 83.39581 85.93556 assigned negative charge : -477.0169 centred at (gu) : 88.40978 82.96272 85.34979 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 198155 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28169 grid for indexing accessible points = 1.400000 m= 94871 mr = 142853 m= 31146 mr = 75984 m= 6343 mr = 24180 m= 734 mr = 4434 m= 31 mr = 449 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 3695 time to turn everything in is 1.590000 number of dielectric boundary points 83371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 24096 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) : 1.832658 object centre at (A) : 19.34000 17.37250 25.28500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2173283 7.2654903E-02 midg,1,midg; midg,igrid,midg -0.3396628 6.0588364E-02 1,midg,midg; igrid,midg,midg -0.4955305 0.3650899 gauss-seidel spectral radius is 0.9992647 estimated iterations to convergence 291 setup time was (sec) 1.920000 now iterating at: 17:13:15 rms-change max change #iterations 10.61805 292.3680 at 10iterations 6.250042 153.2309 at 20iterations 3.648410 76.19341 at 30iterations 2.122326 47.77906 at 40iterations 1.230566 24.24306 at 50iterations 0.7140074 14.32674 at 60iterations 0.4122460 8.377913 at 70iterations 0.2389254 4.426832 at 80iterations 0.1375724 2.439322 at 90iterations 7.9393834E-02 1.435697 at 100iterations 4.5797192E-02 0.8197689 at 110iterations 2.6408173E-02 0.4534526 at 120iterations 1.5218578E-02 0.2555366 at 130iterations 8.7524606E-03 0.1537397 at 140iterations 5.0384710E-03 9.0196609E-02 at 150iterations 2.9025339E-03 4.8995972E-02 at 160iterations 1.6712710E-03 2.9800415E-02 at 170iterations 9.6420204E-04 1.7172813E-02 at 180iterations finished qdiffx linear iterations at : 17:13:26 total time elapsed so far: 13.69000 # loops : 180 mean,max change (kT/e) : 9.6420204E-04 1.7172813E-02 energy calculations done at 13.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.88000 DelPhi exited at 17:13:27 13.879u 0.270s 0:14.46 97.7% 0+0k 0+0io 0pf+0w