Wed Dec 21 14:21:44 PST 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 Wed Dec 21 2011 at 14:21:45 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5741750 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): -35.07200 10.22800 ymin,ymax (A): 1.093000 41.03400 zmin,zma (A): -3.022000 58.98000 x,y,z range (A): 45.30000 39.94100 62.00200 scale (grids/A): 0.5741750 object centre (A): -12.42200 21.06350 27.97900 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 292.2259 centred at (gu) : 90.40096 89.58602 89.85200 assigned negative charge : -290.2262 centred at (gu) : 90.29604 89.72877 89.83941 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4255 nv = 96 ne = 84 npr = 40615 no. pairs analyzed = 40615 no. exposed pairs = 2455 no. arc points = 17258 no. surface atoms = 839 nbur = 1125 mkacc time = 7.0000008E-02 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 = 1.512000 m= 184 mr = 2263 m= 0 mr = 8 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 2168 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1755 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 5387 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0234645E-10 4.7719062E-10 midg,1,midg; midg,igrid,midg 2.2144675E-09 -1.2420508E-09 1,midg,midg; igrid,midg,midg -8.2706880E-10 1.7288765E-09 gauss-seidel spectral radius is 0.9842619 estimated iterations to convergence 65 setup time was (sec) 0.3900000 now iterating at: 14:21:45 rms-change max change #iterations 7.4102513E-02 13.12440 at 10iterations 5.6606289E-03 1.022858 at 20iterations 4.2802820E-04 7.4113846E-02 at 30iterations 3.1873813E-05 6.6928864E-03 at 40iterations 2.4390931E-06 4.2343140E-04 at 50iterations finished qdiffx linear iterations at : 14:21:50 total time elapsed so far: 4.610000 # loops : 50 mean,max change (kT/e) : 2.4390931E-06 4.2343140E-04 energy calculations done at 4.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.740000 DelPhi exited at 14:22:19 4.739u 0.242s 0:35.63 13.9% 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 Wed Dec 21 2011 at 14:22:22 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.722525 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): -35.07200 10.22800 ymin,ymax (A): 1.093000 41.03400 zmin,zma (A): -3.022000 58.98000 x,y,z range (A): 45.30000 39.94100 62.00200 scale (grids/A): 1.722525 object centre (A): -12.42200 21.06350 27.97900 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 292.2259 centred at (gu) : 91.20274 88.75813 89.55576 assigned negative charge : -290.2262 centred at (gu) : 90.88847 89.18636 89.51827 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 46574 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17258 grid for indexing accessible points = 1.400000 m= 15067 mr = 31423 m= 1787 mr = 10963 m= 52 mr = 1013 m= 0 mr = 7 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 421 time to turn everything in is 0.2500000 number of dielectric boundary points 20074 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 14218 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) : 0.5741750 object centre at (A) : -12.42200 21.06350 27.97900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1718286E-02 2.0997902E-02 midg,1,midg; midg,igrid,midg 2.0183537E-03 -7.6638968E-03 1,midg,midg; igrid,midg,midg -3.0948799E-03 -8.6974551E-04 gauss-seidel spectral radius is 0.9982516 estimated iterations to convergence 190 setup time was (sec) 0.4900000 now iterating at: 14:22:24 rms-change max change #iterations 2.956309 154.3166 at 10iterations 1.240704 62.40382 at 20iterations 0.5279521 22.42200 at 30iterations 0.2239135 9.106147 at 40iterations 9.4787650E-02 4.313629 at 50iterations 4.0048596E-02 1.752221 at 60iterations 1.6999392E-02 0.6785908 at 70iterations 7.1899127E-03 0.3084583 at 80iterations 3.0384068E-03 0.1191292 at 90iterations 1.2923062E-03 5.0322711E-02 at 100iterations 5.4942432E-04 2.2575378E-02 at 110iterations 2.3220114E-04 1.1341095E-02 at 120iterations finished qdiffx linear iterations at : 14:22:34 total time elapsed so far: 10.54000 # loops : 120 mean,max change (kT/e) : 2.3220114E-04 1.1341095E-02 energy calculations done at 10.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.66000 DelPhi exited at 14:22:48 10.661u 0.324s 0:26.23 41.8% 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 Wed Dec 21 2011 at 14:22:49 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.583787 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): -35.07200 10.22800 ymin,ymax (A): 1.093000 41.03400 zmin,zma (A): -3.022000 58.98000 x,y,z range (A): 45.30000 39.94100 62.00200 scale (grids/A): 2.583787 object centre (A): -12.42200 21.06350 27.97900 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 292.2259 centred at (gu) : 91.80414 88.13718 89.33367 assigned negative charge : -290.2262 centred at (gu) : 91.33273 88.77956 89.27759 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 107808 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17258 grid for indexing accessible points = 1.400000 m= 50828 mr = 76280 m= 15889 mr = 41142 m= 2918 mr = 12809 m= 249 mr = 2093 m= 8 mr = 130 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 1302 time to turn everything in is 0.6600000 number of dielectric boundary points 45246 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 14646 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) : 1.722525 object centre at (A) : -12.42200 21.06350 27.97900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2458168 0.2198398 midg,1,midg; midg,igrid,midg -3.7749445E-03 -0.1085868 1,midg,midg; igrid,midg,midg -5.8850143E-02 -4.1602679E-02 gauss-seidel spectral radius is 0.9991238 estimated iterations to convergence 267 setup time was (sec) 1.040000 now iterating at: 14:22:50 rms-change max change #iterations 7.331119 268.5816 at 10iterations 4.054670 109.4942 at 20iterations 2.223465 57.30935 at 30iterations 1.217575 31.01201 at 40iterations 0.6676254 18.20957 at 50iterations 0.3650646 8.104095 at 60iterations 0.1987913 4.659472 at 70iterations 0.1083146 2.645485 at 80iterations 5.9187729E-02 1.327652 at 90iterations 3.2285985E-02 0.7914476 at 100iterations 1.7621577E-02 0.4392033 at 110iterations 9.5904563E-03 0.2131882 at 120iterations 5.2238880E-03 0.1313686 at 130iterations 2.8550674E-03 6.6277504E-02 at 140iterations 1.5575552E-03 3.5612583E-02 at 150iterations 8.5067982E-04 1.9861341E-02 at 160iterations 4.6357841E-04 1.0071278E-02 at 170iterations 2.5228414E-04 6.0462952E-03 at 180iterations finished qdiffx linear iterations at : 14:23:05 total time elapsed so far: 15.83000 # loops : 180 mean,max change (kT/e) : 2.5228414E-04 6.0462952E-03 energy calculations done at 15.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.95000 DelPhi exited at 14:23:08 15.957u 0.479s 0:19.36 84.8% 0+0k 0+0io 0pf+0w