Sat Oct 8 18:24:55 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 Sat Oct 8 2011 at 18:24:55 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3268 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5549753 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): -14.55900 44.68800 ymin,ymax (A): -71.59900 -7.452000 zmin,zma (A): -21.74100 25.75000 x,y,z range (A): 59.24700 64.14700 47.49100 scale (grids/A): 0.5549753 object centre (A): 15.06450 -39.52550 2.004499 number of atom coordinates read : 3268 total number of charged atoms : 3124 net assigned charge : -4.999982 assigned positive charge : 489.9718 centred at (gu) : 89.84954 90.60455 89.65900 assigned negative charge : -494.9730 centred at (gu) : 89.82796 90.60429 89.64397 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6714 nv = 96 ne = 84 npr = 65195 no. pairs analyzed = 65195 no. exposed pairs = 4142 no. arc points = 28424 no. surface atoms = 1403 nbur = 1865 mkacc time = 0.1700000 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 = 1.540000 m= 291 mr = 3661 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3337 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2870 ## 368 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8616 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.4522232E-10 -2.6346972E-10 midg,1,midg; midg,igrid,midg -3.8342302E-10 -5.0411186E-10 1,midg,midg; igrid,midg,midg -6.8680955E-10 -2.1047826E-10 gauss-seidel spectral radius is 0.9832779 estimated iterations to convergence 64 setup time was (sec) 0.6600000 now iterating at: 18:24:56 rms-change max change #iterations 8.5369021E-02 12.25636 at 10iterations 5.9507615E-03 0.9635830 at 20iterations 4.4828877E-04 6.1766148E-02 at 30iterations 5.5524786E-05 1.1887550E-02 at 40iterations 1.3768479E-05 3.3855438E-03 at 50iterations finished qdiffx linear iterations at : 18:24:59 total time elapsed so far: 4.480000 # loops : 50 mean,max change (kT/e) : 1.3768479E-05 3.3855438E-03 energy calculations done at 4.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.650000 DelPhi exited at 18:25:00 4.651u 0.407s 0:05.32 94.9% 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 Sat Oct 8 2011 at 18:25:00 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3268 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.664926 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): -14.55900 44.68800 ymin,ymax (A): -71.59900 -7.452000 zmin,zma (A): -21.74100 25.75000 x,y,z range (A): 59.24700 64.14700 47.49100 scale (grids/A): 1.664926 object centre (A): 15.06450 -39.52550 2.004499 number of atom coordinates read : 3268 total number of charged atoms : 3124 net assigned charge : -4.999982 assigned positive charge : 489.9718 centred at (gu) : 89.54802 91.81276 88.97606 assigned negative charge : -494.9730 centred at (gu) : 89.48362 91.81245 88.93148 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74335 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28424 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24476 mr = 51857 m= 2811 mr = 17271 m= 97 mr = 1421 m= 0 mr = 15 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 31155 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 295 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 24039 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) : 0.5549753 object centre at (A) : 15.06450 -39.52550 2.004499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1524220E-03 -5.8349255E-03 midg,1,midg; midg,igrid,midg 7.8954976E-03 1.3616510E-02 1,midg,midg; igrid,midg,midg -2.2749331E-02 -2.4494568E-03 gauss-seidel spectral radius is 0.9982884 estimated iterations to convergence 192 setup time was (sec) 0.9700000 now iterating at: 18:25:01 rms-change max change #iterations 3.685683 173.4167 at 10iterations 1.566938 55.92134 at 20iterations 0.6726832 28.49487 at 30iterations 0.2881202 10.11666 at 40iterations 0.1228973 4.319534 at 50iterations 5.2672751E-02 1.938565 at 60iterations 2.2574475E-02 0.7678833 at 70iterations 9.6860547E-03 0.3535156 at 80iterations 4.1362247E-03 0.1451511 at 90iterations 1.7813442E-03 5.9917688E-02 at 100iterations 7.6253212E-04 2.5775909E-02 at 110iterations 3.3216475E-04 1.2393951E-02 at 120iterations finished qdiffx linear iterations at : 18:25:11 total time elapsed so far: 10.91000 # loops : 120 mean,max change (kT/e) : 3.3216475E-04 1.2393951E-02 energy calculations done at 10.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.08000 DelPhi exited at 18:25:12 11.088u 0.441s 0:11.82 97.4% 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 Sat Oct 8 2011 at 18:25:12 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3268 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.497389 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): -14.55900 44.68800 ymin,ymax (A): -71.59900 -7.452000 zmin,zma (A): -21.74100 25.75000 x,y,z range (A): 59.24700 64.14700 47.49100 scale (grids/A): 2.497389 object centre (A): 15.06450 -39.52550 2.004499 number of atom coordinates read : 3268 total number of charged atoms : 3124 net assigned charge : -4.999982 assigned positive charge : 489.9718 centred at (gu) : 89.32184 92.71899 88.46373 assigned negative charge : -494.9730 centred at (gu) : 89.22540 92.71867 88.39718 start vw surface at 0.1300000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 172547 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28424 grid for indexing accessible points = 1.400000 m= 83730 mr = 126367 m= 25088 mr = 67341 m= 4404 mr = 19127 m= 375 mr = 2957 m= 8 mr = 174 m= 0 mr = 0 time to grow re-entrant surface = 0.9300001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.500000 number of dielectric boundary points 70186 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 24969 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) : 1.664926 object centre at (A) : 15.06450 -39.52550 2.004499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9367191E-02 -6.2643938E-02 midg,1,midg; midg,igrid,midg 0.3396945 0.4073937 1,midg,midg; igrid,midg,midg -0.2895272 -2.4899106E-02 gauss-seidel spectral radius is 0.9991769 estimated iterations to convergence 275 setup time was (sec) 1.820000 now iterating at: 18:25:14 rms-change max change #iterations 9.400661 280.2720 at 10iterations 5.336258 132.2882 at 20iterations 3.013681 64.65591 at 30iterations 1.705259 37.74882 at 40iterations 0.9570681 19.69530 at 50iterations 0.5370826 13.46378 at 60iterations 0.3006831 5.852117 at 70iterations 0.1676976 3.763332 at 80iterations 9.3903035E-02 1.883344 at 90iterations 5.2480083E-02 1.096352 at 100iterations 2.9293323E-02 0.6044121 at 110iterations 1.6394438E-02 0.3216743 at 120iterations 9.1303689E-03 0.1747131 at 130iterations 5.0852317E-03 0.1060934 at 140iterations 2.8468873E-03 5.8285236E-02 at 150iterations 1.5898327E-03 2.8868198E-02 at 160iterations 8.8942191E-04 1.6732216E-02 at 170iterations 4.9990689E-04 1.0223389E-02 at 180iterations finished qdiffx linear iterations at : 18:25:30 total time elapsed so far: 18.12000 # loops : 180 mean,max change (kT/e) : 4.9990689E-04 1.0223389E-02 energy calculations done at 18.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.29000 DelPhi exited at 18:25:31 18.299u 0.486s 0:19.06 98.4% 0+0k 0+0io 0pf+0w