Tue Nov 22 14:12:04 PST 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 Tue Nov 22 2011 at 14:12:07 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1940 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: 0.6379014 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): -35.08300 10.94900 ymin,ymax (A): 1.253000 40.91800 zmin,zma (A): -0.4540000 55.35400 x,y,z range (A): 46.03200 39.66500 55.80800 scale (grids/A): 0.6379014 object centre (A): -12.06700 21.08550 27.45000 number of atom coordinates read : 1940 total number of charged atoms : 1808 net assigned charge : 1.000004 assigned positive charge : 286.3001 centred at (gu) : 90.27808 89.50564 90.11975 assigned negative charge : -285.3003 centred at (gu) : 90.20169 89.60231 90.09812 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5380 nv = 96 ne = 84 npr = 40351 no. pairs analyzed = 40351 no. exposed pairs = 2348 no. arc points = 16619 no. surface atoms = 797 nbur = 1143 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 282 mr = 3047 m= 1 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.2500000 number of dielectric boundary points 2556 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1684 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6368 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3087284E-10 3.1396419E-09 midg,1,midg; midg,igrid,midg 1.0091258E-08 -5.9196972E-09 1,midg,midg; igrid,midg,midg -4.6328883E-09 7.9124209E-09 gauss-seidel spectral radius is 0.9872091 estimated iterations to convergence 72 setup time was (sec) 0.5100000 now iterating at: 14:12:08 rms-change max change #iterations 0.1270672 22.47855 at 10iterations 1.2277726E-02 1.807922 at 20iterations 1.2126352E-03 0.1799421 at 30iterations 1.1738408E-04 1.9073486E-02 at 40iterations 1.1419808E-05 1.6250610E-03 at 50iterations finished qdiffx linear iterations at : 14:12:13 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 1.1419808E-05 1.6250610E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 14:12:14 3.625u 0.188s 0:07.15 53.1% 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 Tue Nov 22 2011 at 14:12:14 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1940 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: 1.913704 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): -35.08300 10.94900 ymin,ymax (A): 1.253000 40.91800 zmin,zma (A): -0.4540000 55.35400 x,y,z range (A): 46.03200 39.66500 55.80800 scale (grids/A): 1.913704 object centre (A): -12.06700 21.08550 27.45000 number of atom coordinates read : 1940 total number of charged atoms : 1808 net assigned charge : 1.000004 assigned positive charge : 286.3001 centred at (gu) : 90.83443 88.51698 90.35947 assigned negative charge : -285.3003 centred at (gu) : 90.60552 88.80711 90.29462 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 57563 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16619 grid for indexing accessible points = 1.400000 m= 21885 mr = 40019 m= 3649 mr = 16993 m= 188 mr = 2520 m= 2 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1628 time to turn everything in is 0.4400000 number of dielectric boundary points 23694 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 14221 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) : 0.6379014 object centre at (A) : -12.06700 21.08550 27.45000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8129327E-03 1.1884441E-02 midg,1,midg; midg,igrid,midg 2.5240779E-03 -1.0829140E-02 1,midg,midg; igrid,midg,midg -1.6783389E-03 -2.4217472E-03 gauss-seidel spectral radius is 0.9985697 estimated iterations to convergence 210 setup time was (sec) 0.7300000 now iterating at: 14:12:15 rms-change max change #iterations 3.625853 162.3612 at 10iterations 1.664686 59.61658 at 20iterations 0.7716869 26.16276 at 30iterations 0.3557661 13.77566 at 40iterations 0.1625606 5.997383 at 50iterations 7.4750461E-02 2.942689 at 60iterations 3.4396626E-02 1.312115 at 70iterations 1.5782231E-02 0.5847168 at 80iterations 7.3078778E-03 0.2498741 at 90iterations 3.3545985E-03 0.1104527 at 100iterations 1.5365196E-03 5.5130959E-02 at 110iterations 7.0850609E-04 2.5220156E-02 at 120iterations finished qdiffx linear iterations at : 14:12:34 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 7.0850609E-04 2.5220156E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 14:12:38 7.641u 0.179s 0:24.13 32.3% 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 Tue Nov 22 2011 at 14:12:42 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1940 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: 2.870556 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): -35.08300 10.94900 ymin,ymax (A): 1.253000 40.91800 zmin,zma (A): -0.4540000 55.35400 x,y,z range (A): 46.03200 39.66500 55.80800 scale (grids/A): 2.870556 object centre (A): -12.06700 21.08550 27.45000 number of atom coordinates read : 1940 total number of charged atoms : 1808 net assigned charge : 1.000004 assigned positive charge : 286.3001 centred at (gu) : 91.25159 87.77536 90.53919 assigned negative charge : -285.3003 centred at (gu) : 90.90839 88.21072 90.44190 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 132482 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16619 grid for indexing accessible points = 1.400000 m= 69471 mr = 96037 m= 27073 mr = 58242 m= 6851 mr = 22870 m= 971 mr = 5505 m= 38 mr = 744 m= 0 mr = 17 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 5587 time to turn everything in is 1.110000 number of dielectric boundary points 53471 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 14464 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) : 1.913704 object centre at (A) : -12.06700 21.08550 27.45000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1445189 4.0732216E-02 midg,1,midg; midg,igrid,midg -6.2889503E-03 -0.1400470 1,midg,midg; igrid,midg,midg -5.1936727E-02 -8.9197189E-02 gauss-seidel spectral radius is 0.9992244 estimated iterations to convergence 283 setup time was (sec) 1.430000 now iterating at: 14:12:49 rms-change max change #iterations 8.463222 331.0519 at 10iterations 4.824546 125.7927 at 20iterations 2.739645 65.36198 at 30iterations 1.555302 32.98556 at 40iterations 0.8813081 18.68887 at 50iterations 0.4999793 10.36053 at 60iterations 0.2821103 5.962650 at 70iterations 0.1600076 3.011795 at 80iterations 9.0105705E-02 1.866699 at 90iterations 5.1010814E-02 1.028573 at 100iterations 2.8879251E-02 0.5669675 at 110iterations 1.6302433E-02 0.3305216 at 120iterations 9.2611974E-03 0.1785736 at 130iterations 5.2188504E-03 0.1049538 at 140iterations 2.9610395E-03 5.9688568E-02 at 150iterations 1.6743947E-03 3.3546448E-02 at 160iterations 9.4408466E-04 1.8417358E-02 at 170iterations 5.3512299E-04 1.0108948E-02 at 180iterations finished qdiffx linear iterations at : 14:13:25 total time elapsed so far: 12.99000 # loops : 180 mean,max change (kT/e) : 5.3512299E-04 1.0108948E-02 energy calculations done at 12.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.17000 DelPhi exited at 14:13:30 13.170u 0.212s 0:48.96 27.3% 0+0k 0+0io 0pf+0w