Mon Oct 10 17:03:52 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 17:03:52 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 = 2864 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: 0.6156613 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): -8.605000 48.75300 ymin,ymax (A): -7.814000 39.24600 zmin,zma (A): -1.195000 56.62900 x,y,z range (A): 57.35800 47.06000 57.82400 scale (grids/A): 0.6156613 object centre (A): 20.07400 15.71600 27.71700 number of atom coordinates read : 2864 total number of charged atoms : 2723 net assigned charge : -4.499977 assigned positive charge : 429.7011 centred at (gu) : 89.08569 89.49140 88.76434 assigned negative charge : -434.2022 centred at (gu) : 88.98673 89.36641 88.68063 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7285 nv = 96 ne = 84 npr = 57173 no. pairs analyzed = 57173 no. exposed pairs = 3745 no. arc points = 26109 no. surface atoms = 1265 nbur = 1599 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 336 mr = 3815 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.3300000 number of dielectric boundary points 3795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2629 ## 256 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9010 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1176368E-08 1.8252528E-09 midg,1,midg; midg,igrid,midg -1.2594072E-08 4.5194897E-09 1,midg,midg; igrid,midg,midg -1.1649082E-08 2.7645579E-09 gauss-seidel spectral radius is 0.9863680 estimated iterations to convergence 70 setup time was (sec) 0.5900000 now iterating at: 17:03:53 rms-change max change #iterations 0.1270586 21.15193 at 10iterations 1.1379630E-02 2.057769 at 20iterations 1.0242843E-03 0.1548996 at 30iterations 9.4066374E-05 1.2268066E-02 at 40iterations 8.7635372E-06 1.2969971E-03 at 50iterations finished qdiffx linear iterations at : 17:03:57 total time elapsed so far: 4.450000 # loops : 50 mean,max change (kT/e) : 8.7635372E-06 1.2969971E-03 energy calculations done at 4.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.610000 DelPhi exited at 17:03:59 4.618u 0.416s 0:06.97 72.0% 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 17:03:59 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 = 2864 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: 1.846984 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): -8.605000 48.75300 ymin,ymax (A): -7.814000 39.24600 zmin,zma (A): -1.195000 56.62900 x,y,z range (A): 57.35800 47.06000 57.82400 scale (grids/A): 1.846984 object centre (A): 20.07400 15.71600 27.71700 number of atom coordinates read : 2864 total number of charged atoms : 2723 net assigned charge : -4.499977 assigned positive charge : 429.7011 centred at (gu) : 87.25630 88.47340 86.29240 assigned negative charge : -434.2022 centred at (gu) : 86.95997 88.09888 86.04158 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 79733 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26109 grid for indexing accessible points = 1.400000 m= 26487 mr = 54389 m= 3316 mr = 18496 m= 134 mr = 1719 m= 4 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 1425 time to turn everything in is 0.6400000 number of dielectric boundary points 35053 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 223 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 21367 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) : 0.6156613 object centre at (A) : 20.07400 15.71600 27.71700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6602533E-03 1.7911289E-02 midg,1,midg; midg,igrid,midg -2.5305754E-02 -1.6514814E-03 1,midg,midg; igrid,midg,midg -5.0979197E-02 2.3840932E-02 gauss-seidel spectral radius is 0.9985815 estimated iterations to convergence 210 setup time was (sec) 0.9600000 now iterating at: 17:04:01 rms-change max change #iterations 4.226548 177.3749 at 10iterations 1.937819 65.11475 at 20iterations 0.8952142 27.79082 at 30iterations 0.4110208 13.39576 at 40iterations 0.1890919 6.072578 at 50iterations 8.7356806E-02 2.807079 at 60iterations 4.0246040E-02 1.311690 at 70iterations 1.8584561E-02 0.5576363 at 80iterations 8.5563390E-03 0.2662230 at 90iterations 3.9504129E-03 0.1224594 at 100iterations 1.8215445E-03 5.9834242E-02 at 110iterations 8.4265060E-04 2.5224686E-02 at 120iterations finished qdiffx linear iterations at : 17:04:11 total time elapsed so far: 11.08000 # loops : 120 mean,max change (kT/e) : 8.4265060E-04 2.5224686E-02 energy calculations done at 11.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.24000 DelPhi exited at 17:04:12 11.246u 0.454s 0:12.46 93.8% 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 Mon Oct 10 2011 at 17:04:12 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 = 2864 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: 2.770476 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): -8.605000 48.75300 ymin,ymax (A): -7.814000 39.24600 zmin,zma (A): -1.195000 56.62900 x,y,z range (A): 57.35800 47.06000 57.82400 scale (grids/A): 2.770476 object centre (A): 20.07400 15.71600 27.71700 number of atom coordinates read : 2864 total number of charged atoms : 2723 net assigned charge : -4.499977 assigned positive charge : 429.7011 centred at (gu) : 85.88413 87.70982 84.43842 assigned negative charge : -434.2022 centred at (gu) : 85.43970 87.14822 84.06234 start vw surface at 0.1200000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 184788 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26109 grid for indexing accessible points = 1.400000 m= 88135 mr = 132267 m= 28475 mr = 70480 m= 5473 mr = 21703 m= 520 mr = 3623 m= 10 mr = 243 m= 0 mr = 3 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 4970 time to turn everything in is 1.660000 number of dielectric boundary points 79082 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 21778 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) : 1.846984 object centre at (A) : 20.07400 15.71600 27.71700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2170039 0.4305928 midg,1,midg; midg,igrid,midg -0.2274400 -6.4905658E-02 1,midg,midg; igrid,midg,midg -0.6276405 0.3357053 gauss-seidel spectral radius is 0.9992620 estimated iterations to convergence 290 setup time was (sec) 1.990000 now iterating at: 17:04:15 rms-change max change #iterations 10.30603 307.8882 at 10iterations 6.120344 149.6291 at 20iterations 3.597554 83.72255 at 30iterations 2.101906 50.48714 at 40iterations 1.224284 25.41637 at 50iterations 0.7097404 14.32999 at 60iterations 0.4116113 7.836458 at 70iterations 0.2381626 4.577712 at 80iterations 0.1376515 2.790440 at 90iterations 7.9467878E-02 1.730009 at 100iterations 4.5784619E-02 0.8676667 at 110iterations 2.6436672E-02 0.4618476 at 120iterations 1.5235918E-02 0.2669184 at 130iterations 8.7635126E-03 0.1555342 at 140iterations 5.0482154E-03 9.4229698E-02 at 150iterations 2.9063020E-03 5.0317764E-02 at 160iterations 1.6744439E-03 3.1562805E-02 at 170iterations 9.6221355E-04 1.8486023E-02 at 180iterations finished qdiffx linear iterations at : 17:04:32 total time elapsed so far: 18.61000 # loops : 180 mean,max change (kT/e) : 9.6221355E-04 1.8486023E-02 energy calculations done at 18.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.78000 DelPhi exited at 17:04:33 18.784u 0.470s 0:20.31 94.7% 0+0k 0+0io 0pf+0w