Tue Oct 11 04:53:54 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 Tue Oct 11 2011 at 04:53:54 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: 283 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 : 425.3858 centred at (gu) : 89.51444 90.52457 91.85515 assigned negative charge : -417.8864 centred at (gu) : 89.47127 90.45702 92.07497 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 1.4050316E-08 -1.4650490E-08 midg,1,midg; midg,igrid,midg 1.3297763E-09 1.2164608E-08 1,midg,midg; igrid,midg,midg 3.5026191E-09 8.2560563E-09 gauss-seidel spectral radius is 0.9865332 estimated iterations to convergence 71 setup time was (sec) 0.4100000 now iterating at: 04:53:54 rms-change max change #iterations 0.1322892 21.81136 at 10iterations 1.2228470E-02 1.704367 at 20iterations 1.1917566E-03 0.1854286 at 30iterations 1.3131180E-04 1.7311096E-02 at 40iterations 2.0875110E-05 3.4484863E-03 at 50iterations finished qdiffx linear iterations at : 04:53:57 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 2.0875110E-05 3.4484863E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 04:53:58 3.443u 0.161s 0:04.36 82.5% 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 04:53:58 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: 283 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 : 425.3858 centred at (gu) : 88.54280 91.57301 95.56506 assigned negative charge : -417.8864 centred at (gu) : 88.41363 91.37083 96.22498 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 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 0.4000000 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 0.4800000 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 5.3644177E-02 -1.9573135E-02 midg,1,midg; midg,igrid,midg -1.4527882E-02 1.7507233E-02 1,midg,midg; igrid,midg,midg 1.1150697E-02 1.9474458E-02 gauss-seidel spectral radius is 0.9986234 estimated iterations to convergence 214 setup time was (sec) 0.6100000 now iterating at: 04:53:59 rms-change max change #iterations 4.263992 164.4791 at 10iterations 1.974631 64.48685 at 20iterations 0.9190538 30.08748 at 30iterations 0.4286849 13.67861 at 40iterations 0.1995935 6.294712 at 50iterations 9.2883393E-02 3.122873 at 60iterations 4.3181475E-02 1.472258 at 70iterations 2.0174427E-02 0.6370106 at 80iterations 9.3846433E-03 0.2833481 at 90iterations 4.3685404E-03 0.1455145 at 100iterations 2.0414824E-03 6.4004898E-02 at 110iterations 9.5461821E-04 2.9437542E-02 at 120iterations finished qdiffx linear iterations at : 04:54:06 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 9.5461821E-04 2.9437542E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 04:54:07 7.942u 0.220s 0:08.57 95.2% 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 Tue Oct 11 2011 at 04:54:07 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: 283 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 : 425.3858 centred at (gu) : 87.81413 92.35948 98.34756 assigned negative charge : -417.8864 centred at (gu) : 87.62032 92.05618 99.33750 start vw surface at 0.1000000 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 = 0.5900000 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 1.140000 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 0.7840155 -9.3722820E-02 midg,1,midg; midg,igrid,midg -0.1816644 2.9730273E-02 1,midg,midg; igrid,midg,midg 0.1782615 0.2988080 gauss-seidel spectral radius is 0.9992805 estimated iterations to convergence 294 setup time was (sec) 1.280000 now iterating at: 04:54:08 rms-change max change #iterations 10.29171 376.2841 at 10iterations 6.144732 142.0683 at 20iterations 3.628170 79.77325 at 30iterations 2.133515 51.01488 at 40iterations 1.248957 23.39991 at 50iterations 0.7281451 13.96957 at 60iterations 0.4245024 8.955879 at 70iterations 0.2469512 4.797586 at 80iterations 0.1433294 2.721861 at 90iterations 8.3239168E-02 1.545855 at 100iterations 4.8233427E-02 0.8573494 at 110iterations 2.7944690E-02 0.5333414 at 120iterations 1.6176492E-02 0.2931938 at 130iterations 9.3728425E-03 0.1813965 at 140iterations 5.4229936E-03 0.1035137 at 150iterations 3.1385550E-03 7.0827484E-02 at 160iterations 1.8149865E-03 3.1964302E-02 at 170iterations 1.0517801E-03 1.9447327E-02 at 180iterations finished qdiffx linear iterations at : 04:54:21 total time elapsed so far: 14.24000 # loops : 180 mean,max change (kT/e) : 1.0517801E-03 1.9447327E-02 energy calculations done at 14.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.37000 DelPhi exited at 04:54:22 14.368u 0.209s 0:15.05 96.7% 0+0k 0+0io 0pf+0w