Tue Nov 22 14:09:56 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+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 Tue Nov 22 2011 at 14:10:00 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6400000 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): -5.196000 34.97100 ymin,ymax (A): -3.632000 49.20300 zmin,zma (A): -24.41900 31.20600 x,y,z range (A): 40.16700 52.83500 55.62500 scale (grids/A): 0.6400000 object centre (A): 14.88750 22.78550 3.393501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.64292 92.34994 90.11250 assigned negative charge : -284.8263 centred at (gu) : 90.74923 92.47354 90.06772 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5523 nv = 96 ne = 84 npr = 40170 no. pairs analyzed = 40170 no. exposed pairs = 2456 no. arc points = 17362 no. surface atoms = 826 nbur = 1138 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 274 mr = 3093 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 40 time to turn everything in is 0.1600000 number of dielectric boundary points 2675 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1705 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6462 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5219959E-10 8.6822416E-09 midg,1,midg; midg,igrid,midg 9.1538475E-09 -1.0235761E-08 1,midg,midg; igrid,midg,midg 1.1873077E-08 -5.1601687E-09 gauss-seidel spectral radius is 0.9872953 estimated iterations to convergence 73 setup time was (sec) 0.3800000 now iterating at: 14:10:03 rms-change max change #iterations 0.1241345 23.95351 at 10iterations 1.2130499E-02 2.311501 at 20iterations 1.2111969E-03 0.1839762 at 30iterations 1.1736302E-04 1.7932892E-02 at 40iterations 1.1683770E-05 1.9168854E-03 at 50iterations finished qdiffx linear iterations at : 14:10:13 total time elapsed so far: 3.720000 # loops : 50 mean,max change (kT/e) : 1.1683770E-05 1.9168854E-03 energy calculations done at 3.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.850000 DelPhi exited at 14:10:15 3.858u 0.222s 0:15.50 26.2% 0+0k 0+0io 3pf+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 14:10:20 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.920000 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): -5.196000 34.97100 ymin,ymax (A): -3.632000 49.20300 zmin,zma (A): -24.41900 31.20600 x,y,z range (A): 40.16700 52.83500 55.62500 scale (grids/A): 1.920000 object centre (A): 14.88750 22.78550 3.393501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 91.92899 97.04958 90.33734 assigned negative charge : -284.8263 centred at (gu) : 92.24774 97.42099 90.20333 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 59201 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17362 grid for indexing accessible points = 1.400000 m= 22217 mr = 40970 m= 3579 mr = 17089 m= 165 mr = 2416 m= 0 mr = 65 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1159 time to turn everything in is 0.3200000 number of dielectric boundary points 24622 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 110 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 14433 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) : 0.6400000 object centre at (A) : 14.88750 22.78550 3.393501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5008156E-02 1.0877897E-02 midg,1,midg; midg,igrid,midg 3.1188125E-02 -6.3426271E-03 1,midg,midg; igrid,midg,midg 8.4777419E-03 -4.4135326E-03 gauss-seidel spectral radius is 0.9985797 estimated iterations to convergence 210 setup time was (sec) 0.5800000 now iterating at: 14:10:25 rms-change max change #iterations 3.590110 153.5834 at 10iterations 1.658024 62.23253 at 20iterations 0.7684242 27.37222 at 30iterations 0.3561002 12.58401 at 40iterations 0.1628722 5.662393 at 50iterations 7.5109467E-02 2.571455 at 60iterations 3.4647197E-02 1.199466 at 70iterations 1.5958220E-02 0.5447617 at 80iterations 7.3587685E-03 0.2583389 at 90iterations 3.4047021E-03 0.1278680 at 100iterations 1.5681431E-03 5.2356005E-02 at 110iterations 7.2345167E-04 2.2476196E-02 at 120iterations finished qdiffx linear iterations at : 14:10:49 total time elapsed so far: 8.480000 # loops : 120 mean,max change (kT/e) : 7.2345167E-04 2.2476196E-02 energy calculations done at 8.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.620000 DelPhi exited at 14:10:50 8.622u 0.236s 0:30.40 29.1% 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 14:10:53 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.880000 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): -5.196000 34.97100 ymin,ymax (A): -3.632000 49.20300 zmin,zma (A): -24.41900 31.20600 x,y,z range (A): 40.16700 52.83500 55.62500 scale (grids/A): 2.880000 object centre (A): 14.88750 22.78550 3.393501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 92.89350 100.5744 90.50603 assigned negative charge : -284.8263 centred at (gu) : 93.37160 101.1314 90.30515 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 136892 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17362 grid for indexing accessible points = 1.400000 m= 70860 mr = 99137 m= 27194 mr = 59062 m= 6619 mr = 22816 m= 851 mr = 5327 m= 47 mr = 584 m= 0 mr = 23 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 3903 time to turn everything in is 0.8000000 number of dielectric boundary points 55514 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 14656 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) : 1.920000 object centre at (A) : 14.88750 22.78550 3.393501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.069471 1.9403303E-02 midg,1,midg; midg,igrid,midg 0.3321511 -9.9308990E-02 1,midg,midg; igrid,midg,midg 5.1908221E-02 -2.6910692E-02 gauss-seidel spectral radius is 0.9992301 estimated iterations to convergence 285 setup time was (sec) 1.060000 now iterating at: 14:10:59 rms-change max change #iterations 8.506693 340.9926 at 10iterations 4.880852 115.8488 at 20iterations 2.775822 62.51258 at 30iterations 1.577775 32.20409 at 40iterations 0.8953414 17.85046 at 50iterations 0.5082185 10.74824 at 60iterations 0.2877612 6.282028 at 70iterations 0.1636040 3.102540 at 80iterations 9.2465654E-02 2.034220 at 90iterations 5.2478176E-02 1.027225 at 100iterations 2.9694483E-02 0.6402607 at 110iterations 1.6867639E-02 0.3567410 at 120iterations 9.5360652E-03 0.1753840 at 130iterations 5.4180189E-03 0.1099739 at 140iterations 3.0724462E-03 5.7791710E-02 at 150iterations 1.7408946E-03 3.6308289E-02 at 160iterations 9.8417245E-04 1.9712448E-02 at 170iterations 5.5860943E-04 1.2119293E-02 at 180iterations finished qdiffx linear iterations at : 14:11:36 total time elapsed so far: 13.06000 # loops : 180 mean,max change (kT/e) : 5.5860943E-04 1.2119293E-02 energy calculations done at 13.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.20000 DelPhi exited at 14:11:37 13.198u 0.289s 0:44.00 30.6% 0+0k 0+0io 0pf+0w