Tue Oct 11 08:33:35 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 08:33:35 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2048 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7122991 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): -8.035000 35.74000 ymin,ymax (A): -27.53800 16.31800 zmin,zma (A): -4.492000 45.48700 x,y,z range (A): 43.77500 43.85600 49.97900 scale (grids/A): 0.7122991 object centre (A): 13.85250 -5.610000 20.49750 number of atom coordinates read : 2048 total number of charged atoms : 1911 net assigned charge : 4.500008 assigned positive charge : 305.2659 centred at (gu) : 90.40693 89.90620 91.39980 assigned negative charge : -300.7661 centred at (gu) : 90.14857 89.68671 91.37319 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7254 nv = 96 ne = 84 npr = 40879 no. pairs analyzed = 40879 no. exposed pairs = 2617 no. arc points = 18245 no. surface atoms = 883 nbur = 1165 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 525 mr = 4079 m= 2 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1580 ## 124 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7750 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1757659E-08 7.3388655E-08 midg,1,midg; midg,igrid,midg -7.8300346E-08 1.5309421E-07 1,midg,midg; igrid,midg,midg -9.0586369E-08 1.9014540E-07 gauss-seidel spectral radius is 0.9897289 estimated iterations to convergence 80 setup time was (sec) 0.5000000 now iterating at: 08:33:35 rms-change max change #iterations 0.2050451 28.94681 at 10iterations 2.5872510E-02 3.956757 at 20iterations 3.2584604E-03 0.4128704 at 30iterations 4.3487333E-04 5.6148529E-02 at 40iterations 6.9824375E-05 9.5806122E-03 at 50iterations finished qdiffx linear iterations at : 08:33:38 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 6.9824375E-05 9.5806122E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 08:33:39 3.341u 0.195s 0:04.13 85.4% 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 08:33:39 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2048 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: 2.136897 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): -8.035000 35.74000 ymin,ymax (A): -27.53800 16.31800 zmin,zma (A): -4.492000 45.48700 x,y,z range (A): 43.77500 43.85600 49.97900 scale (grids/A): 2.136897 object centre (A): 13.85250 -5.610000 20.49750 number of atom coordinates read : 2048 total number of charged atoms : 1911 net assigned charge : 4.500008 assigned positive charge : 305.2659 centred at (gu) : 91.22060 89.71865 94.19936 assigned negative charge : -300.7661 centred at (gu) : 90.44572 89.06013 94.11954 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 75701 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18245 grid for indexing accessible points = 1.400000 m= 31272 mr = 52552 m= 6588 mr = 23875 m= 586 mr = 4441 m= 12 mr = 268 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 33023 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15192 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) : 0.7122991 object centre at (A) : 13.85250 -5.610000 20.49750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3355430E-02 1.5426736E-02 midg,1,midg; midg,igrid,midg -1.1266493E-02 4.1677650E-02 1,midg,midg; igrid,midg,midg -3.4573101E-02 7.8616314E-02 gauss-seidel spectral radius is 0.9988544 estimated iterations to convergence 234 setup time was (sec) 0.8900000 now iterating at: 08:33:40 rms-change max change #iterations 4.644963 166.6055 at 10iterations 2.298189 72.92668 at 20iterations 1.149815 35.33604 at 30iterations 0.5758963 18.89263 at 40iterations 0.2870270 8.338312 at 50iterations 0.1431608 4.147909 at 60iterations 7.1477853E-02 2.158863 at 70iterations 3.5653304E-02 1.200525 at 80iterations 1.7868176E-02 0.4980736 at 90iterations 8.9440923E-03 0.2494736 at 100iterations 4.4697095E-03 0.1517401 at 110iterations 2.2485275E-03 6.5903902E-02 at 120iterations finished qdiffx linear iterations at : 08:33:47 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 2.2485275E-03 6.5903902E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 08:33:47 7.774u 0.191s 0:08.25 96.4% 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 08:33:47 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2048 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: 3.205346 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): -8.035000 35.74000 ymin,ymax (A): -27.53800 16.31800 zmin,zma (A): -4.492000 45.48700 x,y,z range (A): 43.77500 43.85600 49.97900 scale (grids/A): 3.205346 object centre (A): 13.85250 -5.610000 20.49750 number of atom coordinates read : 2048 total number of charged atoms : 1911 net assigned charge : 4.500008 assigned positive charge : 305.2659 centred at (gu) : 91.83105 89.57792 96.29910 assigned negative charge : -300.7661 centred at (gu) : 90.66860 88.59023 96.17933 start vw surface at 0.1500000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 174185 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18245 grid for indexing accessible points = 1.400000 m= 95234 mr = 126512 m= 41196 mr = 79013 m= 12592 mr = 34110 m= 2509 mr = 9894 m= 236 mr = 1820 m= 3 mr = 117 m= 0 mr = 2 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.930000 number of dielectric boundary points 74487 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 15288 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) : 2.136897 object centre at (A) : 13.85250 -5.610000 20.49750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2228896 0.3363053 midg,1,midg; midg,igrid,midg -0.1430531 0.2574530 1,midg,midg; igrid,midg,midg -0.3942220 0.6296543 gauss-seidel spectral radius is 0.9993057 estimated iterations to convergence 299 setup time was (sec) 2.250000 now iterating at: 08:33:50 rms-change max change #iterations 10.37264 377.8705 at 10iterations 6.145226 149.5938 at 20iterations 3.644239 75.18391 at 30iterations 2.159672 41.75475 at 40iterations 1.272854 27.79370 at 50iterations 0.7525593 13.97359 at 60iterations 0.4432251 8.457550 at 70iterations 0.2599432 4.542164 at 80iterations 0.1529365 2.707316 at 90iterations 8.9550830E-02 1.611946 at 100iterations 5.2707233E-02 0.9791069 at 110iterations 3.0968038E-02 0.5429211 at 120iterations 1.8207151E-02 0.3313699 at 130iterations 1.0670968E-02 0.1830540 at 140iterations 6.3033630E-03 0.1243992 at 150iterations 3.7290235E-03 6.4632416E-02 at 160iterations 2.2301967E-03 4.1458130E-02 at 170iterations 1.3532598E-03 2.3651123E-02 at 180iterations finished qdiffx linear iterations at : 08:34:02 total time elapsed so far: 14.05000 # loops : 180 mean,max change (kT/e) : 1.3532598E-03 2.3651123E-02 energy calculations done at 14.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.24000 DelPhi exited at 08:34:02 14.239u 0.233s 0:14.93 96.8% 0+0k 0+0io 0pf+0w