Sun Oct 9 10:33:48 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 10:33:48 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2217 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: 0.6408641 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): -1.583000 47.91000 ymin,ymax (A): -24.34000 31.21000 zmin,zma (A): -5.379000 47.44100 x,y,z range (A): 49.49300 55.55000 52.82000 scale (grids/A): 0.6408641 object centre (A): 23.16350 3.435000 21.03100 number of atom coordinates read : 2217 total number of charged atoms : 2080 net assigned charge : 1.500014 assigned positive charge : 324.3854 centred at (gu) : 90.72980 90.09901 91.14500 assigned negative charge : -322.8863 centred at (gu) : 90.72611 89.92446 91.10155 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6275 nv = 96 ne = 84 npr = 44208 no. pairs analyzed = 44208 no. exposed pairs = 3025 no. arc points = 21162 no. surface atoms = 1021 nbur = 1196 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 356 mr = 3240 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.1700000 number of dielectric boundary points 3345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2067 ## 179 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7317 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6596051E-09 8.2726102E-09 midg,1,midg; midg,igrid,midg -1.5144629E-08 1.9582318E-08 1,midg,midg; igrid,midg,midg 1.5597519E-09 2.9568967E-09 gauss-seidel spectral radius is 0.9873611 estimated iterations to convergence 73 setup time was (sec) 0.3700000 now iterating at: 10:33:48 rms-change max change #iterations 0.1321660 19.07647 at 10iterations 1.2949361E-02 2.280064 at 20iterations 1.2512947E-03 0.1835890 at 30iterations 1.2480641E-04 1.8420219E-02 at 40iterations 1.2436925E-05 1.8348694E-03 at 50iterations finished qdiffx linear iterations at : 10:33:51 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.2436925E-05 1.8348694E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 10:33:52 3.308u 0.182s 0:04.01 86.7% 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 10:33:52 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2217 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: 1.922592 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): -1.583000 47.91000 ymin,ymax (A): -24.34000 31.21000 zmin,zma (A): -5.379000 47.44100 x,y,z range (A): 49.49300 55.55000 52.82000 scale (grids/A): 1.922592 object centre (A): 23.16350 3.435000 21.03100 number of atom coordinates read : 2217 total number of charged atoms : 2080 net assigned charge : 1.500014 assigned positive charge : 324.3854 centred at (gu) : 92.18922 90.29655 93.43487 assigned negative charge : -322.8863 centred at (gu) : 92.17862 89.77338 93.30473 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 66990 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21162 grid for indexing accessible points = 1.400000 m= 23691 mr = 44353 m= 4138 mr = 17087 m= 318 mr = 2674 m= 4 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 225 time to turn everything in is 0.3300000 number of dielectric boundary points 30909 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 16384 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) : 0.6408641 object centre at (A) : 23.16350 3.435000 21.03100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4067117E-02 3.8217869E-02 midg,1,midg; midg,igrid,midg -1.7819487E-02 2.4527155E-02 1,midg,midg; igrid,midg,midg -1.3258812E-02 -1.8183559E-02 gauss-seidel spectral radius is 0.9986314 estimated iterations to convergence 214 setup time was (sec) 0.5400000 now iterating at: 10:33:52 rms-change max change #iterations 3.890531 168.6247 at 10iterations 1.812815 73.17292 at 20iterations 0.8479252 27.72375 at 30iterations 0.3981854 13.29022 at 40iterations 0.1853171 6.243962 at 50iterations 8.6716972E-02 2.902000 at 60iterations 4.0367447E-02 1.360607 at 70iterations 1.8912027E-02 0.5919921 at 80iterations 8.8376245E-03 0.2988091 at 90iterations 4.1468330E-03 0.1343408 at 100iterations 1.9306815E-03 6.6130638E-02 at 110iterations 9.0581999E-04 3.1459808E-02 at 120iterations finished qdiffx linear iterations at : 10:33:59 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 9.0581999E-04 3.1459808E-02 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 10:34:00 7.637u 0.208s 0:08.14 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 10:34:00 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2217 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: 2.883888 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): -1.583000 47.91000 ymin,ymax (A): -24.34000 31.21000 zmin,zma (A): -5.379000 47.44100 x,y,z range (A): 49.49300 55.55000 52.82000 scale (grids/A): 2.883888 object centre (A): 23.16350 3.435000 21.03100 number of atom coordinates read : 2217 total number of charged atoms : 2080 net assigned charge : 1.500014 assigned positive charge : 324.3854 centred at (gu) : 93.28370 90.44470 95.15207 assigned negative charge : -322.8863 centred at (gu) : 93.26799 89.66003 94.95708 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 154875 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21162 grid for indexing accessible points = 1.400000 m= 75302 mr = 108411 m= 28507 mr = 60092 m= 7651 mr = 22727 m= 1463 mr = 5838 m= 122 mr = 1051 m= 2 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 792 time to turn everything in is 0.8700000 number of dielectric boundary points 69732 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 16640 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) : 1.922592 object centre at (A) : 23.16350 3.435000 21.03100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2290746 0.4553494 midg,1,midg; midg,igrid,midg -0.1554680 0.2225801 1,midg,midg; igrid,midg,midg -0.1905076 -0.2230753 gauss-seidel spectral radius is 0.9992575 estimated iterations to convergence 290 setup time was (sec) 1.100000 now iterating at: 10:34:01 rms-change max change #iterations 9.131552 367.5349 at 10iterations 5.316400 122.4726 at 20iterations 3.082136 60.19202 at 30iterations 1.778795 36.25702 at 40iterations 1.026641 20.96929 at 50iterations 0.5922772 12.08600 at 60iterations 0.3407713 6.733488 at 70iterations 0.1955411 3.457870 at 80iterations 0.1124473 2.205624 at 90iterations 6.4634316E-02 1.225283 at 100iterations 3.7045967E-02 0.6964030 at 110iterations 2.1305557E-02 0.4197292 at 120iterations 1.2242875E-02 0.2211418 at 130iterations 7.0160204E-03 0.1319370 at 140iterations 4.0327604E-03 8.0633640E-02 at 150iterations 2.3105107E-03 4.6108246E-02 at 160iterations 1.3273760E-03 2.3891449E-02 at 170iterations 7.6182350E-04 1.5445709E-02 at 180iterations finished qdiffx linear iterations at : 10:34:14 total time elapsed so far: 13.40000 # loops : 180 mean,max change (kT/e) : 7.6182350E-04 1.5445709E-02 energy calculations done at 13.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.53000 DelPhi exited at 10:34:14 13.529u 0.207s 0:14.18 96.7% 0+0k 0+0io 0pf+0w