Sat Oct 8 21:28:31 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 Sat Oct 8 2011 at 21:28:31 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2016 !!! WARNING: HIR 237 has a net charge of 0.5140 !!! WARNING: GLM 283 has a net charge of -0.0940 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: 0.6732351 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): 6.904000 59.78300 ymin,ymax (A): 77.34000 124.0690 zmin,zma (A): -7.364000 33.69600 x,y,z range (A): 52.87900 46.72900 41.06000 scale (grids/A): 0.6732351 object centre (A): 33.34350 100.7045 13.16600 number of atom coordinates read : 2016 total number of charged atoms : 1876 net assigned charge : -7.9996467E-02 assigned positive charge : 301.0728 centred at (gu) : 88.12838 90.14547 90.94810 assigned negative charge : -301.1529 centred at (gu) : 88.24680 90.12564 90.89136 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6346 nv = 96 ne = 84 npr = 40394 no. pairs analyzed = 40394 no. exposed pairs = 2508 no. arc points = 17682 no. surface atoms = 853 nbur = 1163 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 3542 m= 2 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3157 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1563 ## 127 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7043 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0767316E-08 1.3541056E-08 midg,1,midg; midg,igrid,midg -5.0165809E-09 3.3884242E-09 1,midg,midg; igrid,midg,midg 3.5647290E-08 -1.8011894E-08 gauss-seidel spectral radius is 0.9885109 estimated iterations to convergence 76 setup time was (sec) 0.4100000 now iterating at: 21:28:32 rms-change max change #iterations 0.1672056 23.69585 at 10iterations 1.8298572E-02 3.466827 at 20iterations 2.0495742E-03 0.2853184 at 30iterations 2.3673171E-04 3.2001495E-02 at 40iterations 3.0824860E-05 4.3802261E-03 at 50iterations finished qdiffx linear iterations at : 21:28:35 total time elapsed so far: 3.660000 # loops : 50 mean,max change (kT/e) : 3.0824860E-05 4.3802261E-03 energy calculations done at 3.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.790000 DelPhi exited at 21:28:36 3.796u 0.225s 0:04.30 93.2% 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 21:28:36 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2016 !!! WARNING: HIR 237 has a net charge of 0.5140 !!! WARNING: GLM 283 has a net charge of -0.0940 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: 2.019705 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): 6.904000 59.78300 ymin,ymax (A): 77.34000 124.0690 zmin,zma (A): -7.364000 33.69600 x,y,z range (A): 52.87900 46.72900 41.06000 scale (grids/A): 2.019705 object centre (A): 33.34350 100.7045 13.16600 number of atom coordinates read : 2016 total number of charged atoms : 1876 net assigned charge : -7.9996467E-02 assigned positive charge : 301.0728 centred at (gu) : 84.38490 90.43636 92.84433 assigned negative charge : -301.1529 centred at (gu) : 84.74033 90.37675 92.67387 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 67304 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17682 grid for indexing accessible points = 1.400000 m= 26112 mr = 46836 m= 4813 mr = 19522 m= 378 mr = 3113 m= 7 mr = 169 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 28974 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 14838 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) : 0.6732351 object centre at (A) : 33.34350 100.7045 13.16600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0121577E-03 1.1183180E-02 midg,1,midg; midg,igrid,midg 3.1992272E-03 2.1316968E-02 1,midg,midg; igrid,midg,midg -2.7306236E-02 -2.8870242E-02 gauss-seidel spectral radius is 0.9987223 estimated iterations to convergence 222 setup time was (sec) 0.6400000 now iterating at: 21:28:36 rms-change max change #iterations 4.182321 229.3405 at 10iterations 2.013952 74.03909 at 20iterations 0.9639574 34.84580 at 30iterations 0.4647045 16.41765 at 40iterations 0.2236436 7.772789 at 50iterations 0.1073709 3.466801 at 60iterations 5.1683646E-02 1.835854 at 70iterations 2.4816737E-02 0.8415060 at 80iterations 1.1964428E-02 0.4564209 at 90iterations 5.7411324E-03 0.1935730 at 100iterations 2.7601307E-03 8.7692261E-02 at 110iterations 1.3277945E-03 4.3008804E-02 at 120iterations finished qdiffx linear iterations at : 21:28:45 total time elapsed so far: 8.910000 # loops : 120 mean,max change (kT/e) : 1.3277945E-03 4.3008804E-02 energy calculations done at 8.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.040000 DelPhi exited at 21:28:45 9.043u 0.265s 0:09.66 96.2% 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 21:28:45 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2016 !!! WARNING: HIR 237 has a net charge of 0.5140 !!! WARNING: GLM 283 has a net charge of -0.0940 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: 3.029558 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): 6.904000 59.78300 ymin,ymax (A): 77.34000 124.0690 zmin,zma (A): -7.364000 33.69600 x,y,z range (A): 52.87900 46.72900 41.06000 scale (grids/A): 3.029558 object centre (A): 33.34350 100.7045 13.16600 number of atom coordinates read : 2016 total number of charged atoms : 1876 net assigned charge : -7.9996467E-02 assigned positive charge : 301.0728 centred at (gu) : 81.57727 90.65472 94.26630 assigned negative charge : -301.1529 centred at (gu) : 82.11047 90.56503 94.01083 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 155384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17682 grid for indexing accessible points = 1.400000 m= 82033 mr = 113102 m= 32308 mr = 67822 m= 8999 mr = 26148 m= 1613 mr = 6887 m= 130 mr = 1138 m= 4 mr = 71 m= 0 mr = 4 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9500000 number of dielectric boundary points 65299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 15008 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) : 2.019705 object centre at (A) : 33.34350 100.7045 13.16600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6054424E-02 0.1318568 midg,1,midg; midg,igrid,midg -5.9018824E-02 0.1844016 1,midg,midg; igrid,midg,midg -0.3816671 -0.2222368 gauss-seidel spectral radius is 0.9992704 estimated iterations to convergence 292 setup time was (sec) 1.230000 now iterating at: 21:28:47 rms-change max change #iterations 9.556503 362.7670 at 10iterations 5.606447 160.1707 at 20iterations 3.270722 75.52998 at 30iterations 1.910214 40.06548 at 40iterations 1.112109 22.61348 at 50iterations 0.6448432 12.40026 at 60iterations 0.3742042 7.101099 at 70iterations 0.2170236 4.428532 at 80iterations 0.1256815 2.296033 at 90iterations 7.2789900E-02 1.368317 at 100iterations 4.2075068E-02 0.8152771 at 110iterations 2.4352176E-02 0.4682589 at 120iterations 1.4074090E-02 0.2622986 at 130iterations 8.1341267E-03 0.1515303 at 140iterations 4.7043329E-03 8.5172653E-02 at 150iterations 2.7329102E-03 5.2185059E-02 at 160iterations 1.5859499E-03 2.8801441E-02 at 170iterations 9.2405651E-04 1.8999934E-02 at 180iterations finished qdiffx linear iterations at : 21:29:00 total time elapsed so far: 14.45000 # loops : 180 mean,max change (kT/e) : 9.2405651E-04 1.8999934E-02 energy calculations done at 14.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.57000 DelPhi exited at 21:29:00 14.575u 0.304s 0:15.14 98.2% 0+0k 0+0io 0pf+0w