Sun Oct 9 13:22:05 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 Sun Oct 9 2011 at 13:22:05 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 = 2366 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: 0.7022804 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): 22.09900 72.79100 ymin,ymax (A): -14.29200 36.11400 zmin,zma (A): 1.895000 45.07700 x,y,z range (A): 50.69200 50.40600 43.18200 scale (grids/A): 0.7022804 object centre (A): 47.44500 10.91100 23.48600 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 89.35245 91.52663 90.79457 assigned negative charge : -356.4896 centred at (gu) : 89.36277 91.69001 90.85027 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7824 nv = 96 ne = 84 npr = 47653 no. pairs analyzed = 47653 no. exposed pairs = 2979 no. arc points = 20730 no. surface atoms = 1004 nbur = 1362 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 492 mr = 4332 m= 5 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3910 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1893 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8825 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7546166E-08 -6.9542533E-10 midg,1,midg; midg,igrid,midg 8.0260136E-08 -7.6369169E-08 1,midg,midg; igrid,midg,midg 3.7262232E-08 1.9983853E-08 gauss-seidel spectral radius is 0.9894625 estimated iterations to convergence 79 setup time was (sec) 0.3700000 now iterating at: 13:22:05 rms-change max change #iterations 0.2054309 27.43219 at 10iterations 2.5224352E-02 3.132671 at 20iterations 3.4577714E-03 0.4376221 at 30iterations 7.1230379E-04 0.1001968 at 40iterations 2.2261194E-04 3.2991409E-02 at 50iterations finished qdiffx linear iterations at : 13:22:08 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 2.2261194E-04 3.2991409E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 13:22:09 3.349u 0.179s 0:03.78 92.8% 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 Sun Oct 9 2011 at 13:22:09 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 = 2366 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: 2.106841 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): 22.09900 72.79100 ymin,ymax (A): -14.29200 36.11400 zmin,zma (A): 1.895000 45.07700 x,y,z range (A): 50.69200 50.40600 43.18200 scale (grids/A): 2.106841 object centre (A): 47.44500 10.91100 23.48600 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 88.05666 94.57955 92.38322 assigned negative charge : -356.4896 centred at (gu) : 88.08821 95.06985 92.55063 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 83297 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20730 grid for indexing accessible points = 1.400000 m= 32989 mr = 58130 m= 6048 mr = 24475 m= 541 mr = 3929 m= 8 mr = 286 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 368 time to turn everything in is 0.4200000 number of dielectric boundary points 36063 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 17649 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) : 0.7022804 object centre at (A) : 47.44500 10.91100 23.48600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0602095E-02 1.3360420E-02 midg,1,midg; midg,igrid,midg 1.0886620E-02 -6.1975177E-02 1,midg,midg; igrid,midg,midg 4.0693149E-02 -8.8516241E-03 gauss-seidel spectral radius is 0.9988486 estimated iterations to convergence 233 setup time was (sec) 0.6400000 now iterating at: 13:22:10 rms-change max change #iterations 4.930892 236.9726 at 10iterations 2.443025 86.59447 at 20iterations 1.215840 37.50832 at 30iterations 0.6039628 17.97897 at 40iterations 0.3023798 8.495625 at 50iterations 0.1509245 5.007828 at 60iterations 7.5245112E-02 2.624878 at 70iterations 3.7553478E-02 1.168022 at 80iterations 1.8950064E-02 0.6228456 at 90iterations 9.6089225E-03 0.2744236 at 100iterations 4.9283835E-03 0.1464462 at 110iterations 2.6193375E-03 7.5836182E-02 at 120iterations finished qdiffx linear iterations at : 13:22:17 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 2.6193375E-03 7.5836182E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 13:22:17 7.849u 0.188s 0:08.31 96.5% 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 13:22:17 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 = 2366 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: 3.160262 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): 22.09900 72.79100 ymin,ymax (A): -14.29200 36.11400 zmin,zma (A): 1.895000 45.07700 x,y,z range (A): 50.69200 50.40600 43.18200 scale (grids/A): 3.160262 object centre (A): 47.44500 10.91100 23.48600 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 87.08498 96.86915 93.57474 assigned negative charge : -356.4896 centred at (gu) : 87.13222 97.60472 93.82587 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 192077 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20730 grid for indexing accessible points = 1.400000 m= 102414 mr = 140148 m= 41076 mr = 84063 m= 11513 mr = 33490 m= 2226 mr = 8755 m= 282 mr = 1666 m= 9 mr = 198 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 1238 time to turn everything in is 1.260000 number of dielectric boundary points 81277 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 17796 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) : 2.106841 object centre at (A) : 47.44500 10.91100 23.48600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5954495 -2.7537337E-02 midg,1,midg; midg,igrid,midg 0.2242097 -0.5522761 1,midg,midg; igrid,midg,midg 0.3408712 -0.3838635 gauss-seidel spectral radius is 0.9993035 estimated iterations to convergence 299 setup time was (sec) 1.500000 now iterating at: 13:22:19 rms-change max change #iterations 11.07847 323.7668 at 10iterations 6.613247 142.5689 at 20iterations 3.927132 74.03989 at 30iterations 2.329654 45.29339 at 40iterations 1.379337 23.59075 at 50iterations 0.8142422 15.87842 at 60iterations 0.4789045 8.171661 at 70iterations 0.2825739 4.877775 at 80iterations 0.1656005 2.881201 at 90iterations 9.7666301E-02 1.665648 at 100iterations 5.7508841E-02 0.9394379 at 110iterations 3.3982057E-02 0.5460892 at 120iterations 2.0277249E-02 0.3638840 at 130iterations 1.2281489E-02 0.2411175 at 140iterations 7.6858969E-03 0.1649876 at 150iterations 5.0295633E-03 0.1009750 at 160iterations 3.5051780E-03 7.5683594E-02 at 170iterations 2.6067840E-03 5.4229736E-02 at 180iterations finished qdiffx linear iterations at : 13:22:30 total time elapsed so far: 12.93000 # loops : 180 mean,max change (kT/e) : 2.6067840E-03 5.4229736E-02 energy calculations done at 12.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.05000 DelPhi exited at 13:22:31 13.051u 0.217s 0:13.53 98.0% 0+0k 0+0io 0pf+0w