Mon Oct 10 19:31:39 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 Mon Oct 10 2011 at 19:31:39 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 = 2418 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: 0.7116299 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): -14.63800 32.32800 ymin,ymax (A): -6.705000 40.30100 zmin,zma (A): 36.21900 86.24500 x,y,z range (A): 46.96600 47.00600 50.02600 scale (grids/A): 0.7116299 object centre (A): 8.844999 16.79800 61.23200 number of atom coordinates read : 2418 total number of charged atoms : 2281 net assigned charge : 1.000006 assigned positive charge : 360.5208 centred at (gu) : 89.04021 91.57904 88.69959 assigned negative charge : -359.5215 centred at (gu) : 89.19465 91.57370 88.66270 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8650 nv = 96 ne = 84 npr = 48290 no. pairs analyzed = 48290 no. exposed pairs = 3178 no. arc points = 21965 no. surface atoms = 1054 nbur = 1364 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 649 mr = 4810 m= 5 mr = 139 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2800000 number of dielectric boundary points 4355 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1967 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 9351 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8943361E-08 2.4454925E-08 midg,1,midg; midg,igrid,midg 3.9818016E-09 1.6105284E-08 1,midg,midg; igrid,midg,midg 1.2490737E-07 -7.3531822E-08 gauss-seidel spectral radius is 0.9897503 estimated iterations to convergence 80 setup time was (sec) 0.5200000 now iterating at: 19:31:40 rms-change max change #iterations 0.2189660 35.42054 at 10iterations 2.7766125E-02 3.295090 at 20iterations 3.8024192E-03 0.4746838 at 30iterations 9.0265035E-04 0.1134605 at 40iterations 3.6536707E-04 4.3790817E-02 at 50iterations finished qdiffx linear iterations at : 19:31:43 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 3.6536707E-04 4.3790817E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 19:31:43 3.318u 0.173s 0:04.02 86.5% 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 Mon Oct 10 2011 at 19:31:43 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 = 2418 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: 2.134890 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): -14.63800 32.32800 ymin,ymax (A): -6.705000 40.30100 zmin,zma (A): 36.21900 86.24500 x,y,z range (A): 46.96600 47.00600 50.02600 scale (grids/A): 2.134890 object centre (A): 8.844999 16.79800 61.23200 number of atom coordinates read : 2418 total number of charged atoms : 2281 net assigned charge : 1.000006 assigned positive charge : 360.5208 centred at (gu) : 87.12008 94.73653 86.09810 assigned negative charge : -359.5215 centred at (gu) : 87.58375 94.72089 85.98791 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 90570 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21965 grid for indexing accessible points = 1.400000 m= 37841 mr = 63144 m= 8521 mr = 28623 m= 884 mr = 5848 m= 26 mr = 453 m= 0 mr = 5 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 410 time to turn everything in is 0.6800000 number of dielectric boundary points 39769 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 18150 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) : 0.7116299 object centre at (A) : 8.844999 16.79800 61.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0279718E-02 2.7972622E-02 midg,1,midg; midg,igrid,midg -3.4013439E-03 -8.2124872E-03 1,midg,midg; igrid,midg,midg 3.2698687E-02 -2.1182181E-02 gauss-seidel spectral radius is 0.9988852 estimated iterations to convergence 237 setup time was (sec) 0.9800000 now iterating at: 19:31:45 rms-change max change #iterations 5.099184 187.8171 at 10iterations 2.569755 84.40817 at 20iterations 1.293644 37.34107 at 30iterations 0.6511673 18.28125 at 40iterations 0.3291717 9.202726 at 50iterations 0.1661839 4.624084 at 60iterations 8.3529696E-02 2.309391 at 70iterations 4.2254858E-02 1.153770 at 80iterations 2.1510784E-02 0.6383457 at 90iterations 1.0937251E-02 0.3026838 at 100iterations 5.6743780E-03 0.1577530 at 110iterations 3.0224640E-03 8.6202621E-02 at 120iterations finished qdiffx linear iterations at : 19:31:51 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 3.0224640E-03 8.6202621E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 19:31:52 7.728u 0.217s 0:08.24 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 Mon Oct 10 2011 at 19:31:52 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 = 2418 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: 3.202335 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): -14.63800 32.32800 ymin,ymax (A): -6.705000 40.30100 zmin,zma (A): 36.21900 86.24500 x,y,z range (A): 46.96600 47.00600 50.02600 scale (grids/A): 3.202335 object centre (A): 8.844999 16.79800 61.23200 number of atom coordinates read : 2418 total number of charged atoms : 2281 net assigned charge : 1.000006 assigned positive charge : 360.5208 centred at (gu) : 85.68002 97.10484 84.14700 assigned negative charge : -359.5215 centred at (gu) : 86.37562 97.08117 83.98191 start vw surface at 0.1500000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 208745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21965 grid for indexing accessible points = 1.400000 m= 114153 mr = 152232 m= 50657 mr = 94585 m= 16388 mr = 41833 m= 3672 mr = 12789 m= 462 mr = 2657 m= 23 mr = 306 m= 0 mr = 13 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 1278 time to turn everything in is 2.090000 number of dielectric boundary points 89685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 18244 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) : 2.134890 object centre at (A) : 8.844999 16.79800 61.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2330125 0.6326168 midg,1,midg; midg,igrid,midg -0.1540685 -5.8914579E-02 1,midg,midg; igrid,midg,midg 0.2049939 -0.2100130 gauss-seidel spectral radius is 0.9993232 estimated iterations to convergence 303 setup time was (sec) 2.410000 now iterating at: 19:31:54 rms-change max change #iterations 11.37007 357.9344 at 10iterations 6.823264 129.8231 at 20iterations 4.094458 73.85944 at 30iterations 2.444256 44.66223 at 40iterations 1.455932 23.94347 at 50iterations 0.8660265 15.83531 at 60iterations 0.5138073 8.617615 at 70iterations 0.3049985 5.482997 at 80iterations 0.1803536 2.861511 at 90iterations 0.1067527 1.739695 at 100iterations 6.3152045E-02 1.102770 at 110iterations 3.7317134E-02 0.5915527 at 120iterations 2.2150772E-02 0.3608952 at 130iterations 1.3197242E-02 0.2144833 at 140iterations 7.9205334E-03 0.1248894 at 150iterations 4.8510814E-03 7.8490257E-02 at 160iterations 3.0784982E-03 5.1217079E-02 at 170iterations 2.0624993E-03 3.4816742E-02 at 180iterations finished qdiffx linear iterations at : 19:32:06 total time elapsed so far: 14.34000 # loops : 180 mean,max change (kT/e) : 2.0624993E-03 3.4816742E-02 energy calculations done at 14.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.53000 DelPhi exited at 19:32:07 14.530u 0.234s 0:15.31 96.4% 0+0k 0+0io 0pf+0w