Sun Oct 9 16:27:31 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 16:27:31 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3194 !!! WARNING: HIR 108 has a net charge of 0.5140 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: 0.5084915 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): -36.15200 12.00700 ymin,ymax (A): 31.47400 85.15800 zmin,zma (A): -16.80300 53.20800 x,y,z range (A): 48.15900 53.68401 70.01100 scale (grids/A): 0.5084915 object centre (A): -12.07250 58.31600 18.20250 number of atom coordinates read : 3194 total number of charged atoms : 3052 net assigned charge : 2.514009 assigned positive charge : 498.1615 centred at (gu) : 90.33580 88.90302 90.22449 assigned negative charge : -495.6486 centred at (gu) : 90.39349 88.79681 90.12840 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5332 nv = 96 ne = 84 npr = 62287 no. pairs analyzed = 62287 no. exposed pairs = 4261 no. arc points = 30066 no. surface atoms = 1449 nbur = 1745 mkacc time = 0.1200000 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 = 1.680000 m= 155 mr = 2538 m= 0 mr = 4 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2978 ## 462 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7094 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1773132E-10 2.0231360E-10 midg,1,midg; midg,igrid,midg -1.9196081E-10 1.5458859E-10 1,midg,midg; igrid,midg,midg 1.1779676E-10 -6.6632817E-11 gauss-seidel spectral radius is 0.9801178 estimated iterations to convergence 59 setup time was (sec) 0.4300000 now iterating at: 16:27:32 rms-change max change #iterations 5.3425137E-02 9.446124 at 10iterations 2.9410257E-03 0.5097427 at 20iterations 1.9919589E-04 2.8907776E-02 at 30iterations 2.3359240E-05 2.7637482E-03 at 40iterations 3.8680328E-06 4.1246414E-04 at 50iterations finished qdiffx linear iterations at : 16:27:35 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 3.8680328E-06 4.1246414E-04 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 16:27:35 3.566u 0.496s 0:04.42 91.6% 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 Sun Oct 9 2011 at 16:27:35 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3194 !!! WARNING: HIR 108 has a net charge of 0.5140 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: 1.525475 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): -36.15200 12.00700 ymin,ymax (A): 31.47400 85.15800 zmin,zma (A): -16.80300 53.20800 x,y,z range (A): 48.15900 53.68401 70.01100 scale (grids/A): 1.525475 object centre (A): -12.07250 58.31600 18.20250 number of atom coordinates read : 3194 total number of charged atoms : 3052 net assigned charge : 2.514009 assigned positive charge : 498.1615 centred at (gu) : 91.00648 86.70831 90.67281 assigned negative charge : -495.6486 centred at (gu) : 91.17995 86.39027 90.38477 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 60045 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30066 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 15413 mr = 39048 m= 1115 mr = 9631 m= 25 mr = 376 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 27543 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 421 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 22826 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) : 0.5084915 object centre at (A) : -12.07250 58.31600 18.20250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2269648E-02 1.0015870E-02 midg,1,midg; midg,igrid,midg -3.0569050E-03 2.4497494E-04 1,midg,midg; igrid,midg,midg 2.1782089E-03 1.9835785E-03 gauss-seidel spectral radius is 0.9979372 estimated iterations to convergence 175 setup time was (sec) 0.5600000 now iterating at: 16:27:36 rms-change max change #iterations 3.021373 166.2225 at 10iterations 1.186427 53.99550 at 20iterations 0.4676396 18.76013 at 30iterations 0.1845150 7.869160 at 40iterations 7.2416194E-02 2.885507 at 50iterations 2.8487708E-02 1.097047 at 60iterations 1.1214269E-02 0.3997540 at 70iterations 4.4221045E-03 0.1762576 at 80iterations 1.7395682E-03 7.4268341E-02 at 90iterations 6.8654807E-04 2.9701233E-02 at 100iterations 2.7240551E-04 1.0844231E-02 at 110iterations 1.0764019E-04 4.0359497E-03 at 120iterations finished qdiffx linear iterations at : 16:27:44 total time elapsed so far: 8.340000 # loops : 120 mean,max change (kT/e) : 1.0764019E-04 4.0359497E-03 energy calculations done at 8.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.480000 DelPhi exited at 16:27:45 8.484u 0.240s 0:09.20 94.7% 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 Sun Oct 9 2011 at 16:27:45 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3194 !!! WARNING: HIR 108 has a net charge of 0.5140 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: 2.288212 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): -36.15200 12.00700 ymin,ymax (A): 31.47400 85.15800 zmin,zma (A): -16.80300 53.20800 x,y,z range (A): 48.15900 53.68401 70.01100 scale (grids/A): 2.288212 object centre (A): -12.07250 58.31600 18.20250 number of atom coordinates read : 3194 total number of charged atoms : 3052 net assigned charge : 2.514009 assigned positive charge : 498.1615 centred at (gu) : 91.50931 85.06216 91.00901 assigned negative charge : -495.6486 centred at (gu) : 91.76968 84.58510 90.57701 start vw surface at 0.1100000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 140106 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30066 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 57585 mr = 96564 m= 12330 mr = 43512 m= 1421 mr = 8368 m= 72 mr = 728 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 62333 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 24355 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) : 1.525475 object centre at (A) : -12.07250 58.31600 18.20250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2100880 0.1535640 midg,1,midg; midg,igrid,midg -2.5496740E-02 -7.0568845E-03 1,midg,midg; igrid,midg,midg 2.8082123E-02 3.4001935E-02 gauss-seidel spectral radius is 0.9990744 estimated iterations to convergence 260 setup time was (sec) 0.9500000 now iterating at: 16:27:46 rms-change max change #iterations 8.416046 350.3472 at 10iterations 4.686492 140.7020 at 20iterations 2.579757 67.64368 at 30iterations 1.414571 33.83669 at 40iterations 0.7726437 17.86180 at 50iterations 0.4198839 10.21606 at 60iterations 0.2279925 5.944733 at 70iterations 0.1231091 2.952336 at 80iterations 6.6746898E-02 1.570871 at 90iterations 3.6003619E-02 0.8699265 at 100iterations 1.9389957E-02 0.4811268 at 110iterations 1.0484555E-02 0.2282391 at 120iterations 5.6355880E-03 0.1396179 at 130iterations 3.0279022E-03 7.5471878E-02 at 140iterations 1.6289736E-03 3.8241386E-02 at 150iterations 8.7575050E-04 1.9010544E-02 at 160iterations 4.7130475E-04 1.0253906E-02 at 170iterations 2.5307958E-04 5.4264069E-03 at 180iterations finished qdiffx linear iterations at : 16:27:57 total time elapsed so far: 12.16000 # loops : 180 mean,max change (kT/e) : 2.5307958E-04 5.4264069E-03 energy calculations done at 12.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.30000 DelPhi exited at 16:27:58 12.306u 0.249s 0:12.89 97.2% 0+0k 0+0io 0pf+0w