Sun Oct 9 15:22:25 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 Sun Oct 9 2011 at 15:22:25 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4422 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5436360 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): 70.92101 130.2590 ymin,ymax (A): -11.95200 49.74900 zmin,zma (A): -5.524000 59.96100 x,y,z range (A): 59.33798 61.70100 65.48500 scale (grids/A): 0.5436360 object centre (A): 100.5900 18.89850 27.21850 number of atom coordinates read : 4422 total number of charged atoms : 4270 net assigned charge : 5.000022 assigned positive charge : 673.0446 centred at (gu) : 89.69257 91.51109 92.39503 assigned negative charge : -668.0490 centred at (gu) : 89.65813 91.49697 92.34631 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8319 nv = 96 ne = 84 npr = 89733 no. pairs analyzed = 89733 no. exposed pairs = 5100 no. arc points = 35953 no. surface atoms = 1721 nbur = 2701 mkacc time = 0.1900000 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 = 1.568000 m= 334 mr = 4604 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 61 time to turn everything in is 0.4200000 number of dielectric boundary points 4037 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3549 ## 442 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 10985 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.2435941E-11 1.2909499E-09 midg,1,midg; midg,igrid,midg 9.9260232E-11 5.7439509E-10 1,midg,midg; igrid,midg,midg -4.9770323E-11 5.3616994E-10 gauss-seidel spectral radius is 0.9826587 estimated iterations to convergence 63 setup time was (sec) 0.6300000 now iterating at: 15:22:26 rms-change max change #iterations 9.1792963E-02 12.01132 at 10iterations 7.8522619E-03 1.086430 at 20iterations 2.5447218E-03 0.3714943 at 30iterations 1.2242894E-03 0.1786137 at 40iterations 5.9577421E-04 8.6999893E-02 at 50iterations finished qdiffx linear iterations at : 15:22:29 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 5.9577421E-04 8.6999893E-02 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 15:22:29 3.220u 0.150s 0:03.69 91.3% 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 Sun Oct 9 2011 at 15:22:29 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4422 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.630908 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): 70.92101 130.2590 ymin,ymax (A): -11.95200 49.74900 zmin,zma (A): -5.524000 59.96100 x,y,z range (A): 59.33798 61.70100 65.48500 scale (grids/A): 1.630908 object centre (A): 100.5900 18.89850 27.21850 number of atom coordinates read : 4422 total number of charged atoms : 4270 net assigned charge : 5.000022 assigned positive charge : 673.0446 centred at (gu) : 89.07607 94.53179 97.18347 assigned negative charge : -668.0490 centred at (gu) : 88.97408 94.49052 97.03877 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 93522 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35953 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 29042 mr = 66236 m= 3057 mr = 20443 m= 80 mr = 1599 m= 0 mr = 6 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 3418 time to turn everything in is 0.6100000 number of dielectric boundary points 37417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 386 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 32729 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) : 0.5436360 object centre at (A) : 100.5900 18.89850 27.21850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2755296E-03 3.9694104E-02 midg,1,midg; midg,igrid,midg -1.9794094E-04 4.0626149E-03 1,midg,midg; igrid,midg,midg -1.2285901E-02 6.8741338E-03 gauss-seidel spectral radius is 0.9983096 estimated iterations to convergence 193 setup time was (sec) 0.8700000 now iterating at: 15:22:30 rms-change max change #iterations 4.198788 176.0851 at 10iterations 1.807079 57.43266 at 20iterations 0.7768404 21.68032 at 30iterations 0.3348227 10.31793 at 40iterations 0.1444589 4.006084 at 50iterations 6.2597662E-02 1.856523 at 60iterations 2.7521627E-02 0.8214302 at 70iterations 1.2508298E-02 0.3824825 at 80iterations 6.1647934E-03 0.2063847 at 90iterations 3.5242313E-03 0.1170731 at 100iterations 2.3314198E-03 7.4459076E-02 at 110iterations 1.6979291E-03 5.0174713E-02 at 120iterations finished qdiffx linear iterations at : 15:22:36 total time elapsed so far: 6.820000 # loops : 120 mean,max change (kT/e) : 1.6979291E-03 5.0174713E-02 energy calculations done at 6.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.000000 DelPhi exited at 15:22:37 7.007u 0.166s 0:07.45 96.1% 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 Sun Oct 9 2011 at 15:22:37 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4422 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.446362 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): 70.92101 130.2590 ymin,ymax (A): -11.95200 49.74900 zmin,zma (A): -5.524000 59.96100 x,y,z range (A): 59.33798 61.70100 65.48500 scale (grids/A): 2.446362 object centre (A): 100.5900 18.89850 27.21850 number of atom coordinates read : 4422 total number of charged atoms : 4270 net assigned charge : 5.000022 assigned positive charge : 673.0446 centred at (gu) : 88.61335 96.79720 100.7747 assigned negative charge : -668.0490 centred at (gu) : 88.46102 96.73566 100.5579 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 217670 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35953 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 101558 mr = 161758 m= 28964 mr = 81535 m= 4809 mr = 22152 m= 351 mr = 3253 m= 8 mr = 157 m= 0 mr = 2 time to grow re-entrant surface = 0.8600001 no. cavity mid-points inaccessible to solvent = 11326 time to turn everything in is 1.460000 number of dielectric boundary points 84503 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 34127 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) : 1.630908 object centre at (A) : 100.5900 18.89850 27.21850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2273795 0.5784266 midg,1,midg; midg,igrid,midg -2.2286041E-02 1.4340444E-02 1,midg,midg; igrid,midg,midg -0.1423305 0.1152698 gauss-seidel spectral radius is 0.9992026 estimated iterations to convergence 280 setup time was (sec) 1.750000 now iterating at: 15:22:39 rms-change max change #iterations 10.90011 296.0873 at 10iterations 6.329857 134.4512 at 20iterations 3.654903 78.01546 at 30iterations 2.096444 51.44331 at 40iterations 1.199108 24.39545 at 50iterations 0.6810592 12.51413 at 60iterations 0.3872089 7.131090 at 70iterations 0.2199378 4.120514 at 80iterations 0.1244765 2.389458 at 90iterations 7.0465893E-02 1.418539 at 100iterations 3.9886177E-02 0.7144318 at 110iterations 2.2528291E-02 0.4124298 at 120iterations 1.2783893E-02 0.2189636 at 130iterations 7.2795800E-03 0.1285858 at 140iterations 4.1851141E-03 7.4956894E-02 at 150iterations 2.4510687E-03 4.6120644E-02 at 160iterations 1.4949284E-03 2.9891968E-02 at 170iterations 9.7346248E-04 1.9306183E-02 at 180iterations finished qdiffx linear iterations at : 15:22:48 total time elapsed so far: 11.44000 # loops : 180 mean,max change (kT/e) : 9.7346248E-04 1.9306183E-02 energy calculations done at 11.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.61000 DelPhi exited at 15:22:49 11.614u 0.199s 0:12.09 97.6% 0+0k 0+0io 0pf+0w