Sat Oct 8 11:34:32 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 Sat Oct 8 2011 at 11:34:32 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 = 4284 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: 0.5847473 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): -25.46900 35.41200 ymin,ymax (A): 38.07700 97.66900 zmin,zma (A): 30.82600 90.66400 x,y,z range (A): 60.88100 59.59200 59.83800 scale (grids/A): 0.5847473 object centre (A): 4.971501 67.87300 60.74500 number of atom coordinates read : 4284 total number of charged atoms : 4126 net assigned charge : -0.9999640 assigned positive charge : 641.2735 centred at (gu) : 90.57470 88.16087 88.43292 assigned negative charge : -642.2766 centred at (gu) : 90.45287 88.31311 88.56788 start vw surface at 0.2000000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 9249 nv = 96 ne = 84 npr = 91508 no. pairs analyzed = 91508 no. exposed pairs = 4696 no. arc points = 31363 no. surface atoms = 1598 nbur = 2686 mkacc time = 0.2600000 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= 444 mr = 5507 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 121 time to turn everything in is 0.5200000 number of dielectric boundary points 4138 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3308 ## 355 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 12217 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4508674E-09 -3.8441206E-09 midg,1,midg; midg,igrid,midg 7.8486808E-09 -4.0389541E-09 1,midg,midg; igrid,midg,midg -4.4087800E-09 4.5428097E-09 gauss-seidel spectral radius is 0.9849911 estimated iterations to convergence 67 setup time was (sec) 0.8100000 now iterating at: 11:34:33 rms-change max change #iterations 0.1244381 16.31743 at 10iterations 1.0294902E-02 1.354799 at 20iterations 1.0718270E-03 0.1368713 at 30iterations 2.2333582E-04 3.0977383E-02 at 40iterations 7.3163166E-05 1.0904312E-02 at 50iterations finished qdiffx linear iterations at : 11:34:37 total time elapsed so far: 4.230000 # loops : 50 mean,max change (kT/e) : 7.3163166E-05 1.0904312E-02 energy calculations done at 4.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.420000 DelPhi exited at 11:34:37 4.424u 0.285s 0:05.39 87.1% 0+0k 0+0io 6pf+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 Sat Oct 8 2011 at 11:34:38 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 = 4284 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: 1.754242 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): -25.46900 35.41200 ymin,ymax (A): 38.07700 97.66900 zmin,zma (A): 30.82600 90.66400 x,y,z range (A): 60.88100 59.59200 59.83800 scale (grids/A): 1.754242 object centre (A): 4.971501 67.87300 60.74500 number of atom coordinates read : 4284 total number of charged atoms : 4126 net assigned charge : -0.9999640 assigned positive charge : 641.2735 centred at (gu) : 91.72258 84.48157 85.29766 assigned negative charge : -642.2766 centred at (gu) : 91.35802 84.93912 85.70347 start vw surface at 0.2100000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 102735 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31363 grid for indexing accessible points = 1.400000 m= 36052 mr = 75124 m= 4828 mr = 27401 m= 174 mr = 3013 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 6158 time to turn everything in is 0.9000000 number of dielectric boundary points 38216 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 307 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 32061 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) : 0.5847473 object centre at (A) : 4.971501 67.87300 60.74500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0409777E-02 -2.7829517E-02 midg,1,midg; midg,igrid,midg 3.7727591E-02 -1.0528540E-02 1,midg,midg; igrid,midg,midg -1.5082612E-02 4.0588345E-02 gauss-seidel spectral radius is 0.9985346 estimated iterations to convergence 207 setup time was (sec) 1.220000 now iterating at: 11:34:39 rms-change max change #iterations 4.782259 169.8483 at 10iterations 2.168857 64.95465 at 20iterations 0.9919419 25.79515 at 30iterations 0.4518644 12.54808 at 40iterations 0.2070457 5.923881 at 50iterations 9.4640195E-02 2.671349 at 60iterations 4.3242756E-02 1.310715 at 70iterations 1.9799627E-02 0.5407486 at 80iterations 9.0877954E-03 0.2674255 at 90iterations 4.1569984E-03 0.1317291 at 100iterations 1.9258210E-03 5.9925079E-02 at 110iterations 9.0154819E-04 2.6369095E-02 at 120iterations finished qdiffx linear iterations at : 11:34:48 total time elapsed so far: 10.11000 # loops : 120 mean,max change (kT/e) : 9.0154819E-04 2.6369095E-02 energy calculations done at 10.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.30000 DelPhi exited at 11:34:49 10.302u 0.325s 0:11.02 96.3% 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 Sat Oct 8 2011 at 11:34:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4284 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: 2.631363 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): -25.46900 35.41200 ymin,ymax (A): 38.07700 97.66900 zmin,zma (A): 30.82600 90.66400 x,y,z range (A): 60.88100 59.59200 59.83800 scale (grids/A): 2.631363 object centre (A): 4.971501 67.87300 60.74500 number of atom coordinates read : 4284 total number of charged atoms : 4126 net assigned charge : -0.9999640 assigned positive charge : 641.2735 centred at (gu) : 92.58358 81.72207 82.94608 assigned negative charge : -642.2766 centred at (gu) : 92.03695 82.40856 83.55502 start vw surface at 0.2100000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 238517 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31363 grid for indexing accessible points = 1.400000 m= 120747 mr = 181892 m= 40342 mr = 100829 m= 8367 mr = 32880 m= 826 mr = 6329 m= 26 mr = 531 m= 0 mr = 7 time to grow re-entrant surface = 1.380000 no. cavity mid-points inaccessible to solvent = 20887 time to turn everything in is 2.280000 number of dielectric boundary points 86357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 2.450000 number of grid points assigned charge 32989 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) : 1.754242 object centre at (A) : 4.971501 67.87300 60.74500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.069815 -0.3231697 midg,1,midg; midg,igrid,midg 0.4849316 -0.1625545 1,midg,midg; igrid,midg,midg -0.2061926 0.4773501 gauss-seidel spectral radius is 0.9992539 estimated iterations to convergence 289 setup time was (sec) 2.640000 now iterating at: 11:34:52 rms-change max change #iterations 11.60922 314.2057 at 10iterations 6.801833 144.9946 at 20iterations 3.941006 68.41838 at 30iterations 2.287627 37.69598 at 40iterations 1.321933 22.28595 at 50iterations 0.7625697 12.54489 at 60iterations 0.4397776 7.306427 at 70iterations 0.2531888 4.661850 at 80iterations 0.1457890 2.175696 at 90iterations 8.3857104E-02 1.343540 at 100iterations 4.8147034E-02 0.8872471 at 110iterations 2.7710512E-02 0.4645658 at 120iterations 1.5959123E-02 0.2586288 at 130iterations 9.1871694E-03 0.1444511 at 140iterations 5.2931793E-03 0.1025505 at 150iterations 3.0680574E-03 4.9392700E-02 at 160iterations 1.7880035E-03 2.8365612E-02 at 170iterations 1.0534630E-03 1.8613100E-02 at 180iterations finished qdiffx linear iterations at : 11:35:07 total time elapsed so far: 17.62000 # loops : 180 mean,max change (kT/e) : 1.0534630E-03 1.8613100E-02 energy calculations done at 17.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.81000 DelPhi exited at 11:35:07 17.814u 0.336s 0:18.80 96.4% 0+0k 0+0io 0pf+0w