Tue Oct 11 04:53:27 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 04:53:27 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 = 2838 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: 0.6191520 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): -28.57000 25.91100 ymin,ymax (A): -26.26600 27.62100 zmin,zma (A): -0.5139999 56.98400 x,y,z range (A): 54.48100 53.88700 57.49800 scale (grids/A): 0.6191520 object centre (A): -1.329500 0.6775007 28.23500 number of atom coordinates read : 2838 total number of charged atoms : 2695 net assigned charge : 7.500026 assigned positive charge : 422.9859 centred at (gu) : 89.53410 90.51183 91.83061 assigned negative charge : -415.4865 centred at (gu) : 89.48985 90.43788 92.05403 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7663 nv = 96 ne = 84 npr = 53408 no. pairs analyzed = 53408 no. exposed pairs = 4032 no. arc points = 29586 no. surface atoms = 1337 nbur = 1501 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 411 mr = 3732 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2100000 number of dielectric boundary points 4305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2938 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9128 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4226202E-08 -1.4830269E-08 midg,1,midg; midg,igrid,midg 9.5427866E-10 1.2588981E-08 1,midg,midg; igrid,midg,midg 3.4233110E-09 8.3408667E-09 gauss-seidel spectral radius is 0.9865332 estimated iterations to convergence 71 setup time was (sec) 0.4000000 now iterating at: 04:53:27 rms-change max change #iterations 0.1295843 20.81042 at 10iterations 1.2037265E-02 1.743101 at 20iterations 1.1789446E-03 0.1879501 at 30iterations 1.3219439E-04 1.7665863E-02 at 40iterations 2.1479276E-05 3.5438538E-03 at 50iterations finished qdiffx linear iterations at : 04:53:30 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 2.1479276E-05 3.5438538E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 04:53:31 3.445u 0.190s 0:03.99 90.9% 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 Tue Oct 11 2011 at 04:53:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2838 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: 1.857456 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): -28.57000 25.91100 ymin,ymax (A): -26.26600 27.62100 zmin,zma (A): -0.5139999 56.98400 x,y,z range (A): 54.48100 53.88700 57.49800 scale (grids/A): 1.857456 object centre (A): -1.329500 0.6775007 28.23500 number of atom coordinates read : 2838 total number of charged atoms : 2695 net assigned charge : 7.500026 assigned positive charge : 422.9859 centred at (gu) : 88.60181 91.53481 95.49151 assigned negative charge : -415.4865 centred at (gu) : 88.46940 91.31342 96.16219 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 82255 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29586 grid for indexing accessible points = 1.400000 m= 27888 mr = 53513 m= 3969 mr = 18954 m= 179 mr = 2099 m= 5 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 800 time to turn everything in is 0.4100000 number of dielectric boundary points 39686 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 205 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 21129 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) : 0.6191520 object centre at (A) : -1.329500 0.6775007 28.23500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3680737E-02 -2.1595234E-02 midg,1,midg; midg,igrid,midg -1.4682587E-02 1.9000813E-02 1,midg,midg; igrid,midg,midg 1.1096556E-02 1.9465508E-02 gauss-seidel spectral radius is 0.9986234 estimated iterations to convergence 214 setup time was (sec) 0.6300000 now iterating at: 04:53:32 rms-change max change #iterations 4.230819 164.4791 at 10iterations 1.958967 64.51427 at 20iterations 0.9115636 29.02386 at 30iterations 0.4254155 13.36055 at 40iterations 0.1979940 6.277266 at 50iterations 9.2156194E-02 3.140720 at 60iterations 4.2845838E-02 1.445709 at 70iterations 2.0016868E-02 0.6443748 at 80iterations 9.3105836E-03 0.2916794 at 90iterations 4.3361923E-03 0.1443596 at 100iterations 2.0261325E-03 6.2891006E-02 at 110iterations 9.4724784E-04 2.9495239E-02 at 120iterations finished qdiffx linear iterations at : 04:53:39 total time elapsed so far: 7.920000 # loops : 120 mean,max change (kT/e) : 9.4724784E-04 2.9495239E-02 energy calculations done at 7.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 04:53:39 8.061u 0.201s 0:08.62 95.8% 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 04:53:40 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 = 2838 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: 2.786184 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): -28.57000 25.91100 ymin,ymax (A): -26.26600 27.62100 zmin,zma (A): -0.5139999 56.98400 x,y,z range (A): 54.48100 53.88700 57.49800 scale (grids/A): 2.786184 object centre (A): -1.329500 0.6775007 28.23500 number of atom coordinates read : 2838 total number of charged atoms : 2695 net assigned charge : 7.500026 assigned positive charge : 422.9859 centred at (gu) : 87.90269 92.30215 98.23722 assigned negative charge : -415.4865 centred at (gu) : 87.70396 91.97009 99.24331 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 190172 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29586 grid for indexing accessible points = 1.400000 m= 91305 mr = 131062 m= 30643 mr = 71199 m= 6646 mr = 22765 m= 898 mr = 4545 m= 45 mr = 532 m= 0 mr = 8 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 2687 time to turn everything in is 1.030000 number of dielectric boundary points 89598 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 21559 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) : 1.857456 object centre at (A) : -1.329500 0.6775007 28.23500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7843546 -0.1238855 midg,1,midg; midg,igrid,midg -0.1829098 4.4150688E-02 1,midg,midg; igrid,midg,midg 0.1770855 0.2984964 gauss-seidel spectral radius is 0.9992805 estimated iterations to convergence 294 setup time was (sec) 1.280000 now iterating at: 04:53:41 rms-change max change #iterations 10.22416 376.2841 at 10iterations 6.105526 142.0585 at 20iterations 3.605280 78.33017 at 30iterations 2.120645 50.47852 at 40iterations 1.241733 23.82342 at 50iterations 0.7239655 14.03522 at 60iterations 0.4221015 8.991041 at 70iterations 0.2455262 4.834422 at 80iterations 0.1425156 2.708006 at 90iterations 8.2775742E-02 1.548934 at 100iterations 4.7968525E-02 0.8434792 at 110iterations 2.7795106E-02 0.5243282 at 120iterations 1.6088476E-02 0.2950020 at 130iterations 9.3233939E-03 0.1835632 at 140iterations 5.3942399E-03 0.1020432 at 150iterations 3.1223278E-03 7.0476532E-02 at 160iterations 1.8057439E-03 3.1732559E-02 at 170iterations 1.0463211E-03 1.9363403E-02 at 180iterations finished qdiffx linear iterations at : 04:53:53 total time elapsed so far: 13.00000 # loops : 180 mean,max change (kT/e) : 1.0463211E-03 1.9363403E-02 energy calculations done at 13.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.13000 DelPhi exited at 04:53:53 13.131u 0.201s 0:13.86 96.1% 0+0k 0+0io 0pf+0w