Mon Oct 10 10:24:10 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 Mon Oct 10 2011 at 10:24:10 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2823 !!! WARNING: HIT 228 has a net charge of 0.5140 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: 0.5809684 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): -17.72900 33.77700 ymin,ymax (A): -59.95200 -0.8070000 zmin,zma (A): -1.710000 59.56700 x,y,z range (A): 51.50600 59.14500 61.27700 scale (grids/A): 0.5809684 object centre (A): 8.023998 -30.37950 28.92850 number of atom coordinates read : 2823 total number of charged atoms : 2671 net assigned charge : 5.014015 assigned positive charge : 415.8839 centred at (gu) : 88.41757 88.37537 88.17740 assigned negative charge : -410.8703 centred at (gu) : 88.51472 88.27299 88.07652 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6595 nv = 96 ne = 84 npr = 54144 no. pairs analyzed = 54144 no. exposed pairs = 4298 no. arc points = 31343 no. surface atoms = 1418 nbur = 1405 mkacc time = 0.1100000 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 = 1.484000 m= 314 mr = 2853 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 4039 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3085 ## 307 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8125 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5131789E-09 2.1274311E-09 midg,1,midg; midg,igrid,midg -1.4855828E-09 2.2469611E-09 1,midg,midg; igrid,midg,midg 4.6013735E-09 -5.8566879E-10 gauss-seidel spectral radius is 0.9847173 estimated iterations to convergence 66 setup time was (sec) 0.4900000 now iterating at: 10:24:11 rms-change max change #iterations 9.4242133E-02 16.80256 at 10iterations 7.1815304E-03 1.108939 at 20iterations 5.8027176E-04 8.9324951E-02 at 30iterations 4.9187078E-05 7.8811646E-03 at 40iterations 5.3958461E-06 7.6293945E-04 at 50iterations finished qdiffx linear iterations at : 10:24:13 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 5.3958461E-06 7.6293945E-04 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 10:24:14 3.264u 0.205s 0:03.77 91.7% 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 Mon Oct 10 2011 at 10:24:14 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2823 !!! WARNING: HIT 228 has a net charge of 0.5140 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: 1.742905 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): -17.72900 33.77700 ymin,ymax (A): -59.95200 -0.8070000 zmin,zma (A): -1.710000 59.56700 x,y,z range (A): 51.50600 59.14500 61.27700 scale (grids/A): 1.742905 object centre (A): 8.023998 -30.37950 28.92850 number of atom coordinates read : 2823 total number of charged atoms : 2671 net assigned charge : 5.014015 assigned positive charge : 415.8839 centred at (gu) : 85.25211 85.12569 84.53194 assigned negative charge : -410.8703 centred at (gu) : 85.54411 84.81869 84.22916 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70535 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31343 grid for indexing accessible points = 1.400000 m= 21859 mr = 43011 m= 2695 mr = 13794 m= 119 mr = 1057 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 252 time to turn everything in is 0.5000000 number of dielectric boundary points 37339 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 247 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 20732 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) : 0.5809684 object centre at (A) : 8.023998 -30.37950 28.92850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7358431E-03 5.4969988E-03 midg,1,midg; midg,igrid,midg 1.8102871E-02 2.9777151E-02 1,midg,midg; igrid,midg,midg 9.4272122E-03 2.2550728E-03 gauss-seidel spectral radius is 0.9984262 estimated iterations to convergence 200 setup time was (sec) 0.7700000 now iterating at: 10:24:15 rms-change max change #iterations 3.695248 158.6962 at 10iterations 1.627358 70.78956 at 20iterations 0.7139397 25.95868 at 30iterations 0.3160610 11.65238 at 40iterations 0.1387543 5.394388 at 50iterations 6.1407540E-02 2.083862 at 60iterations 2.7164988E-02 0.9809952 at 70iterations 1.2008443E-02 0.4207458 at 80iterations 5.2870605E-03 0.2091370 at 90iterations 2.3347875E-03 8.1180573E-02 at 100iterations 1.0331171E-03 3.8467407E-02 at 110iterations 4.5771903E-04 1.5030861E-02 at 120iterations finished qdiffx linear iterations at : 10:24:21 total time elapsed so far: 7.250000 # loops : 120 mean,max change (kT/e) : 4.5771903E-04 1.5030861E-02 energy calculations done at 7.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.420000 DelPhi exited at 10:24:22 7.419u 0.241s 0:07.94 96.3% 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 Mon Oct 10 2011 at 10:24:22 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2823 !!! WARNING: HIT 228 has a net charge of 0.5140 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: 2.614358 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): -17.72900 33.77700 ymin,ymax (A): -59.95200 -0.8070000 zmin,zma (A): -1.710000 59.56700 x,y,z range (A): 51.50600 59.14500 61.27700 scale (grids/A): 2.614358 object centre (A): 8.023998 -30.37950 28.92850 number of atom coordinates read : 2823 total number of charged atoms : 2671 net assigned charge : 5.014015 assigned positive charge : 415.8839 centred at (gu) : 82.87805 82.68842 81.79771 assigned negative charge : -410.8703 centred at (gu) : 83.31604 82.22796 81.34373 start vw surface at 0.1700000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 162754 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31343 grid for indexing accessible points = 1.400000 m= 72692 mr = 106066 m= 22694 mr = 53985 m= 3994 mr = 15766 m= 301 mr = 2242 m= 13 mr = 85 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 798 time to turn everything in is 1.270000 number of dielectric boundary points 84304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 21360 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) : 1.742905 object centre at (A) : 8.023998 -30.37950 28.92850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2592942E-03 1.6546838E-02 midg,1,midg; midg,igrid,midg 0.3599792 0.4116009 1,midg,midg; igrid,midg,midg 4.0051579E-02 4.5683362E-02 gauss-seidel spectral radius is 0.9992295 estimated iterations to convergence 284 setup time was (sec) 1.560000 now iterating at: 10:24:24 rms-change max change #iterations 9.407789 290.4526 at 10iterations 5.576303 133.6450 at 20iterations 3.248888 80.65291 at 30iterations 1.889457 43.80150 at 40iterations 1.091609 25.62868 at 50iterations 0.6260099 13.76413 at 60iterations 0.3592920 8.298468 at 70iterations 0.2058511 4.393257 at 80iterations 0.1173234 2.389590 at 90iterations 6.7066908E-02 1.499609 at 100iterations 3.8232900E-02 0.8416125 at 110iterations 2.1754919E-02 0.4511013 at 120iterations 1.2378057E-02 0.2674375 at 130iterations 7.0364601E-03 0.1353502 at 140iterations 3.9988696E-03 7.6941907E-02 at 150iterations 2.2720718E-03 4.6846390E-02 at 160iterations 1.2904677E-03 2.4782181E-02 at 170iterations 7.3393801E-04 1.5520096E-02 at 180iterations finished qdiffx linear iterations at : 10:24:35 total time elapsed so far: 13.20000 # loops : 180 mean,max change (kT/e) : 7.3393801E-04 1.5520096E-02 energy calculations done at 13.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.37000 DelPhi exited at 10:24:36 13.369u 0.252s 0:14.05 96.8% 0+0k 0+0io 0pf+0w