Tue Oct 11 00:12:01 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 Tue Oct 11 2011 at 00:12:01 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 = 2564 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5611424 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): -20.02700 31.46300 ymin,ymax (A): 44.73300 108.1750 zmin,zma (A): 35.16000 78.76100 x,y,z range (A): 51.49000 63.44200 43.60100 scale (grids/A): 0.5611424 object centre (A): 5.717999 76.45400 56.96050 number of atom coordinates read : 2564 total number of charged atoms : 2425 net assigned charge : 8.000024 assigned positive charge : 386.5789 centred at (gu) : 88.84792 87.73554 89.68785 assigned negative charge : -378.5795 centred at (gu) : 88.86670 87.82668 89.52608 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5231 nv = 96 ne = 84 npr = 51371 no. pairs analyzed = 51371 no. exposed pairs = 3123 no. arc points = 21441 no. surface atoms = 1061 nbur = 1503 mkacc time = 7.9999998E-02 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= 212 mr = 2836 m= 0 mr = 7 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.2100000 number of dielectric boundary points 2600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2146 ## 269 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 6688 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.0936996E-10 2.2355771E-09 midg,1,midg; midg,igrid,midg 3.0203253E-09 -6.9526112E-12 1,midg,midg; igrid,midg,midg 1.3749669E-09 5.2214083E-10 gauss-seidel spectral radius is 0.9835805 estimated iterations to convergence 64 setup time was (sec) 0.4000000 now iterating at: 00:12:02 rms-change max change #iterations 7.7837683E-02 13.70184 at 10iterations 6.7388462E-03 1.145767 at 20iterations 1.1457388E-03 0.2919159 at 30iterations 3.1016348E-04 8.0226898E-02 at 40iterations 8.7226937E-05 2.2640228E-02 at 50iterations finished qdiffx linear iterations at : 00:12:05 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 8.7226937E-05 2.2640228E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 00:12:06 3.457u 0.175s 0:04.29 84.3% 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 Oct 11 2011 at 00:12:06 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 = 2564 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: 1.683427 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): -20.02700 31.46300 ymin,ymax (A): 44.73300 108.1750 zmin,zma (A): 35.16000 78.76100 x,y,z range (A): 51.49000 63.44200 43.60100 scale (grids/A): 1.683427 object centre (A): 5.717999 76.45400 56.96050 number of atom coordinates read : 2564 total number of charged atoms : 2425 net assigned charge : 8.000024 assigned positive charge : 386.5789 centred at (gu) : 86.54356 83.20608 89.06329 assigned negative charge : -378.5795 centred at (gu) : 86.59980 83.47984 88.57787 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 57779 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21441 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18083 mr = 39913 m= 1932 mr = 12952 m= 67 mr = 1047 m= 0 mr = 11 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 889 time to turn everything in is 0.3100000 number of dielectric boundary points 23938 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 237 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 18704 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) : 0.5611424 object centre at (A) : 5.717999 76.45400 56.96050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5403640E-03 1.4482790E-02 midg,1,midg; midg,igrid,midg -1.1843216E-02 7.6670474E-03 1,midg,midg; igrid,midg,midg 5.4240394E-03 6.0815117E-03 gauss-seidel spectral radius is 0.9982436 estimated iterations to convergence 189 setup time was (sec) 0.5300000 now iterating at: 00:12:06 rms-change max change #iterations 3.219321 145.5947 at 10iterations 1.355893 53.94289 at 20iterations 0.5742286 23.09136 at 30iterations 0.2431136 9.148430 at 40iterations 0.1037115 4.189856 at 50iterations 4.3996245E-02 1.898396 at 60iterations 1.8790480E-02 0.6817513 at 70iterations 8.2400050E-03 0.3166962 at 80iterations 3.7128001E-03 0.1777668 at 90iterations 1.7980242E-03 9.1667175E-02 at 100iterations 9.5528684E-04 5.1605225E-02 at 110iterations 5.4486695E-04 2.8366089E-02 at 120iterations finished qdiffx linear iterations at : 00:12:13 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 5.4486695E-04 2.8366089E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 00:12:14 7.787u 0.185s 0:08.31 95.7% 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 Tue Oct 11 2011 at 00:12:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2564 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.525141 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): -20.02700 31.46300 ymin,ymax (A): 44.73300 108.1750 zmin,zma (A): 35.16000 78.76100 x,y,z range (A): 51.49000 63.44200 43.60100 scale (grids/A): 2.525141 object centre (A): 5.717999 76.45400 56.96050 number of atom coordinates read : 2564 total number of charged atoms : 2425 net assigned charge : 8.000024 assigned positive charge : 386.5789 centred at (gu) : 84.81508 79.80894 88.59477 assigned negative charge : -378.5795 centred at (gu) : 84.89963 80.21974 87.86679 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 134356 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21441 grid for indexing accessible points = 1.400000 m= 62144 mr = 97320 m= 18215 mr = 50223 m= 3157 mr = 14280 m= 211 mr = 2249 m= 8 mr = 105 m= 0 mr = 3 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 3297 time to turn everything in is 0.7000000 number of dielectric boundary points 53911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 19389 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) : 1.683427 object centre at (A) : 5.717999 76.45400 56.96050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4390680E-02 0.1608175 midg,1,midg; midg,igrid,midg -0.4778065 8.5005596E-02 1,midg,midg; igrid,midg,midg 3.4164757E-02 5.6793965E-02 gauss-seidel spectral radius is 0.9991384 estimated iterations to convergence 269 setup time was (sec) 0.9300000 now iterating at: 00:12:15 rms-change max change #iterations 8.062728 356.3933 at 10iterations 4.456481 107.4829 at 20iterations 2.460329 54.85954 at 30iterations 1.358623 30.46017 at 40iterations 0.7498610 18.23766 at 50iterations 0.4131493 8.866282 at 60iterations 0.2267909 5.200539 at 70iterations 0.1249877 2.848011 at 80iterations 6.8686545E-02 1.506557 at 90iterations 3.7929267E-02 0.9397430 at 100iterations 2.1018352E-02 0.5291481 at 110iterations 1.1701135E-02 0.2847328 at 120iterations 6.5767937E-03 0.1593666 at 130iterations 3.7941316E-03 0.1005096 at 140iterations 2.2654941E-03 6.1805725E-02 at 150iterations 1.4256599E-03 4.2915344E-02 at 160iterations 9.5005316E-04 2.9251099E-02 at 170iterations 6.6548708E-04 2.1408081E-02 at 180iterations finished qdiffx linear iterations at : 00:12:26 total time elapsed so far: 11.97000 # loops : 180 mean,max change (kT/e) : 6.6548708E-04 2.1408081E-02 energy calculations done at 11.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.11000 DelPhi exited at 00:12:27 12.108u 0.214s 0:12.85 95.7% 0+0k 0+0io 0pf+0w