Sun Oct 9 22:26:13 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 22:26:14 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 = 3190 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: 0.5739899 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): -26.20300 35.62800 ymin,ymax (A): 5.609000 67.63100 zmin,zma (A): -0.6540000 52.88200 x,y,z range (A): 61.83100 62.02200 53.53600 scale (grids/A): 0.5739899 object centre (A): 4.712500 36.62000 26.11400 number of atom coordinates read : 3190 total number of charged atoms : 3042 net assigned charge : 4.500013 assigned positive charge : 482.1586 centred at (gu) : 92.36761 89.57586 89.16035 assigned negative charge : -477.6600 centred at (gu) : 92.43009 89.64269 89.12270 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6939 nv = 96 ne = 84 npr = 62820 no. pairs analyzed = 62820 no. exposed pairs = 4296 no. arc points = 30892 no. surface atoms = 1432 nbur = 1758 mkacc time = 0.1400000 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 = 1.484000 m= 291 mr = 3412 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3400000 number of dielectric boundary points 3806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3103 ## 387 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8889 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1024530E-10 1.2680337E-09 midg,1,midg; midg,igrid,midg 2.3167666E-09 -4.2005335E-10 1,midg,midg; igrid,midg,midg 1.1605739E-09 -7.2530587E-10 gauss-seidel spectral radius is 0.9843612 estimated iterations to convergence 66 setup time was (sec) 0.5600000 now iterating at: 22:26:14 rms-change max change #iterations 9.6014060E-02 13.11592 at 10iterations 7.3777987E-03 1.164442 at 20iterations 5.5430771E-04 7.9710960E-02 at 30iterations 4.6877914E-05 6.4668655E-03 at 40iterations 6.2237973E-06 8.2492828E-04 at 50iterations finished qdiffx linear iterations at : 22:26:17 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 6.2237973E-06 8.2492828E-04 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 22:26:17 3.182u 0.129s 0:03.61 91.4% 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 22:26:17 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 = 3190 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: 1.721970 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): -26.20300 35.62800 ymin,ymax (A): 5.609000 67.63100 zmin,zma (A): -0.6540000 52.88200 x,y,z range (A): 61.83100 62.02200 53.53600 scale (grids/A): 1.721970 object centre (A): 4.712500 36.62000 26.11400 number of atom coordinates read : 3190 total number of charged atoms : 3042 net assigned charge : 4.500013 assigned positive charge : 482.1586 centred at (gu) : 97.10197 88.72663 87.48029 assigned negative charge : -477.6600 centred at (gu) : 97.28975 88.92775 87.36788 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 75387 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30892 grid for indexing accessible points = 1.400000 m= 23111 mr = 49215 m= 2726 mr = 15479 m= 98 mr = 1386 m= 3 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 83 time to turn everything in is 0.5200000 number of dielectric boundary points 35230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 307 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 23505 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) : 0.5739899 object centre at (A) : 4.712500 36.62000 26.11400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0642503E-03 1.0988958E-02 midg,1,midg; midg,igrid,midg 1.1848775E-03 3.8955254E-03 1,midg,midg; igrid,midg,midg -4.4624601E-03 6.9250478E-03 gauss-seidel spectral radius is 0.9984056 estimated iterations to convergence 199 setup time was (sec) 0.7800000 now iterating at: 22:26:18 rms-change max change #iterations 3.864478 222.0371 at 10iterations 1.696282 62.48496 at 20iterations 0.7444984 25.60908 at 30iterations 0.3268088 11.91870 at 40iterations 0.1434329 5.217534 at 50iterations 6.2821724E-02 2.055095 at 60iterations 2.7816320E-02 1.092255 at 70iterations 1.2189276E-02 0.4461288 at 80iterations 5.3662085E-03 0.1951003 at 90iterations 2.3610876E-03 8.2099915E-02 at 100iterations 1.0395045E-03 3.6875248E-02 at 110iterations 4.5805727E-04 1.5873909E-02 at 120iterations finished qdiffx linear iterations at : 22:26:24 total time elapsed so far: 6.780000 # loops : 120 mean,max change (kT/e) : 4.5805727E-04 1.5873909E-02 energy calculations done at 6.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.950000 DelPhi exited at 22:26:25 6.950u 0.172s 0:07.46 95.4% 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 22:26:25 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 = 3190 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: 2.582955 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): -26.20300 35.62800 ymin,ymax (A): 5.609000 67.63100 zmin,zma (A): -0.6540000 52.88200 x,y,z range (A): 61.83100 62.02200 53.53600 scale (grids/A): 2.582955 object centre (A): 4.712500 36.62000 26.11400 number of atom coordinates read : 3190 total number of charged atoms : 3042 net assigned charge : 4.500013 assigned positive charge : 482.1586 centred at (gu) : 100.6529 88.08972 86.22010 assigned negative charge : -477.6600 centred at (gu) : 100.9346 88.39142 86.05156 start vw surface at 0.1800000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 174890 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30892 grid for indexing accessible points = 1.400000 m= 78623 mr = 121027 m= 23478 mr = 60708 m= 4440 mr = 17466 m= 456 mr = 3022 m= 17 mr = 226 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 288 time to turn everything in is 1.260000 number of dielectric boundary points 79452 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 24325 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) : 1.721970 object centre at (A) : 4.712500 36.62000 26.11400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1453783 0.1634784 midg,1,midg; midg,igrid,midg 2.9375203E-02 -3.0567737E-03 1,midg,midg; igrid,midg,midg -9.3593292E-02 0.2470794 gauss-seidel spectral radius is 0.9992185 estimated iterations to convergence 282 setup time was (sec) 1.540000 now iterating at: 22:26:26 rms-change max change #iterations 9.791043 335.2712 at 10iterations 5.704782 164.4660 at 20iterations 3.295222 79.35360 at 30iterations 1.895433 41.86273 at 40iterations 1.089792 25.94824 at 50iterations 0.6234626 12.90113 at 60iterations 0.3562114 7.432613 at 70iterations 0.2034360 4.998310 at 80iterations 0.1155863 2.269798 at 90iterations 6.5805398E-02 1.352823 at 100iterations 3.7358947E-02 0.7475605 at 110iterations 2.1191645E-02 0.4077520 at 120iterations 1.2023427E-02 0.2335448 at 130iterations 6.8233255E-03 0.1247406 at 140iterations 3.8718616E-03 7.5109959E-02 at 150iterations 2.1876055E-03 4.0967941E-02 at 160iterations 1.2397555E-03 2.4827003E-02 at 170iterations 7.0303812E-04 1.3221741E-02 at 180iterations finished qdiffx linear iterations at : 22:26:36 total time elapsed so far: 10.93000 # loops : 180 mean,max change (kT/e) : 7.0303812E-04 1.3221741E-02 energy calculations done at 10.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.10000 DelPhi exited at 22:26:36 11.105u 0.167s 0:11.55 97.4% 0+0k 0+0io 0pf+0w