Tue Oct 11 05:15:29 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 05:15:29 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2190 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: 0.6912889 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): 19.86700 63.13800 ymin,ymax (A): -3.576000 33.45400 zmin,zma (A): 20.42700 71.92500 x,y,z range (A): 43.27100 37.03000 51.49800 scale (grids/A): 0.6912889 object centre (A): 41.50250 14.93900 46.17600 number of atom coordinates read : 2190 total number of charged atoms : 1902 net assigned charge : 7.500009 assigned positive charge : 306.3000 centred at (gu) : 90.06718 89.78311 89.44986 assigned negative charge : -298.8002 centred at (gu) : 90.24911 89.80828 89.44183 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6583 nv = 96 ne = 84 npr = 39290 no. pairs analyzed = 39290 no. exposed pairs = 2487 no. arc points = 17120 no. surface atoms = 846 nbur = 1344 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 439 mr = 3740 m= 1 mr = 75 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 0.1600000 number of dielectric boundary points 3208 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1666 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 7411 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4779245E-08 4.0987370E-08 midg,1,midg; midg,igrid,midg 5.3350259E-08 3.3268094E-08 1,midg,midg; igrid,midg,midg 1.0008377E-07 -1.8067503E-08 gauss-seidel spectral radius is 0.9890925 estimated iterations to convergence 78 setup time was (sec) 0.3400000 now iterating at: 05:15:30 rms-change max change #iterations 0.1707442 25.56613 at 10iterations 2.0096166E-02 3.023632 at 20iterations 2.4920346E-03 0.3252525 at 30iterations 3.3871343E-04 4.9253941E-02 at 40iterations 6.7688627E-05 9.1476440E-03 at 50iterations finished qdiffx linear iterations at : 05:15:33 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 6.7688627E-05 9.1476440E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 05:15:33 3.374u 0.215s 0:03.92 91.3% 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 05:15:33 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2190 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: 2.073867 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): 19.86700 63.13800 ymin,ymax (A): -3.576000 33.45400 zmin,zma (A): 20.42700 71.92500 x,y,z range (A): 43.27100 37.03000 51.49800 scale (grids/A): 2.073867 object centre (A): 41.50250 14.93900 46.17600 number of atom coordinates read : 2190 total number of charged atoms : 1902 net assigned charge : 7.500009 assigned positive charge : 306.3000 centred at (gu) : 90.20166 89.34943 88.34970 assigned negative charge : -298.8002 centred at (gu) : 90.74728 89.42484 88.32560 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 70018 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17120 grid for indexing accessible points = 1.400000 m= 28030 mr = 49291 m= 5376 mr = 21238 m= 483 mr = 3626 m= 8 mr = 225 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 29535 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 15059 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) : 0.6912889 object centre at (A) : 41.50250 14.93900 46.17600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4993982E-02 3.6803830E-02 midg,1,midg; midg,igrid,midg 2.3121519E-02 1.1720245E-02 1,midg,midg; igrid,midg,midg 3.9876938E-02 1.4219051E-02 gauss-seidel spectral radius is 0.9987800 estimated iterations to convergence 227 setup time was (sec) 0.5700000 now iterating at: 05:15:34 rms-change max change #iterations 4.274332 208.5102 at 10iterations 2.098293 75.09145 at 20iterations 1.017901 37.22664 at 30iterations 0.5013672 15.83471 at 40iterations 0.2442613 7.960991 at 50iterations 0.1199072 3.673443 at 60iterations 5.8627114E-02 1.911786 at 70iterations 2.8741004E-02 0.8866527 at 80iterations 1.3988744E-02 0.4393764 at 90iterations 6.9045098E-03 0.2725356 at 100iterations 3.3945979E-03 0.1060104 at 110iterations 1.6832462E-03 5.2862167E-02 at 120iterations finished qdiffx linear iterations at : 05:15:41 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 1.6832462E-03 5.2862167E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 05:15:42 7.887u 0.210s 0:08.47 95.5% 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 05:15:42 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2190 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: 3.110800 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): 19.86700 63.13800 ymin,ymax (A): -3.576000 33.45400 zmin,zma (A): 20.42700 71.92500 x,y,z range (A): 43.27100 37.03000 51.49800 scale (grids/A): 3.110800 object centre (A): 41.50250 14.93900 46.17600 number of atom coordinates read : 2190 total number of charged atoms : 1902 net assigned charge : 7.500009 assigned positive charge : 306.3000 centred at (gu) : 90.30254 89.02413 87.52455 assigned negative charge : -298.8002 centred at (gu) : 91.12093 89.13740 87.48848 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 161409 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17120 grid for indexing accessible points = 1.400000 m= 87669 mr = 118830 m= 35539 mr = 72915 m= 10111 mr = 29217 m= 1926 mr = 7770 m= 201 mr = 1431 m= 1 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.100000 number of dielectric boundary points 66569 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 15216 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) : 2.073867 object centre at (A) : 41.50250 14.93900 46.17600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3509586 0.2814838 midg,1,midg; midg,igrid,midg 0.1999273 9.5934041E-02 1,midg,midg; igrid,midg,midg 0.3303987 0.2925982 gauss-seidel spectral radius is 0.9992841 estimated iterations to convergence 295 setup time was (sec) 1.330000 now iterating at: 05:15:43 rms-change max change #iterations 9.748391 396.0678 at 10iterations 5.748590 126.5495 at 20iterations 3.380032 71.53732 at 30iterations 1.983126 39.83994 at 40iterations 1.159299 28.90051 at 50iterations 0.6767956 11.93687 at 60iterations 0.3954854 7.515738 at 70iterations 0.2309251 4.559611 at 80iterations 0.1346298 2.341419 at 90iterations 7.8401364E-02 1.441778 at 100iterations 4.5749959E-02 0.8994474 at 110iterations 2.6752230E-02 0.5486693 at 120iterations 1.5642826E-02 0.3205528 at 130iterations 9.2484793E-03 0.1765137 at 140iterations 5.5085095E-03 0.1098213 at 150iterations 3.3441868E-03 6.4676285E-02 at 160iterations 2.1037213E-03 3.9723396E-02 at 170iterations 1.3803479E-03 2.7568817E-02 at 180iterations finished qdiffx linear iterations at : 05:15:55 total time elapsed so far: 12.58000 # loops : 180 mean,max change (kT/e) : 1.3803479E-03 2.7568817E-02 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.72000 DelPhi exited at 05:15:55 12.720u 0.206s 0:13.26 97.4% 0+0k 0+0io 0pf+0w