Sun Oct 9 22:11:42 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 22:11:42 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 = 2576 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6353966 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): -9.044000 45.88100 ymin,ymax (A): -16.49500 39.53300 zmin,zma (A): -3.814000 49.19000 x,y,z range (A): 54.92500 56.02800 53.00400 scale (grids/A): 0.6353966 object centre (A): 18.41850 11.51900 22.68800 number of atom coordinates read : 2576 total number of charged atoms : 2432 net assigned charge : 5.000012 assigned positive charge : 388.4979 centred at (gu) : 91.17238 90.17968 90.21763 assigned negative charge : -383.4987 centred at (gu) : 91.23586 90.15051 90.23604 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6762 nv = 96 ne = 84 npr = 52504 no. pairs analyzed = 52504 no. exposed pairs = 3129 no. arc points = 22117 no. surface atoms = 1058 nbur = 1518 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 331 mr = 3635 m= 3 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 41 time to turn everything in is 0.2000000 number of dielectric boundary points 3425 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2272 ## 263 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8390 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.9417548E-09 4.7853668E-09 midg,1,midg; midg,igrid,midg 3.3593364E-09 9.7645900E-09 1,midg,midg; igrid,midg,midg 1.0015386E-08 -1.6282521E-10 gauss-seidel spectral radius is 0.9871660 estimated iterations to convergence 72 setup time was (sec) 0.3900000 now iterating at: 22:11:42 rms-change max change #iterations 0.1380491 20.80514 at 10iterations 1.3575993E-02 2.011029 at 20iterations 1.3102447E-03 0.1903868 at 30iterations 1.3015485E-04 1.8188715E-02 at 40iterations 1.2551859E-05 1.7700195E-03 at 50iterations finished qdiffx linear iterations at : 22:11:45 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.2551859E-05 1.7700195E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 22:11:46 3.427u 0.179s 0:03.99 89.9% 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 22:11:46 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 = 2576 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.906190 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): -9.044000 45.88100 ymin,ymax (A): -16.49500 39.53300 zmin,zma (A): -3.814000 49.19000 x,y,z range (A): 54.92500 56.02800 53.00400 scale (grids/A): 1.906190 object centre (A): 18.41850 11.51900 22.68800 number of atom coordinates read : 2576 total number of charged atoms : 2432 net assigned charge : 5.000012 assigned positive charge : 388.4979 centred at (gu) : 93.51679 90.53899 90.65246 assigned negative charge : -383.4987 centred at (gu) : 93.70747 90.45156 90.70802 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73773 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22117 grid for indexing accessible points = 1.400000 m= 24373 mr = 50499 m= 3524 mr = 17472 m= 228 mr = 2139 m= 3 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 2381 time to turn everything in is 0.3700000 number of dielectric boundary points 31677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 174 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 19153 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) : 0.6353966 object centre at (A) : 18.41850 11.51900 22.68800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8118055E-02 -7.4717375E-03 midg,1,midg; midg,igrid,midg 2.1804797E-02 -1.7317345E-03 1,midg,midg; igrid,midg,midg -5.4195076E-03 2.0989761E-02 gauss-seidel spectral radius is 0.9986286 estimated iterations to convergence 214 setup time was (sec) 0.5900000 now iterating at: 22:11:47 rms-change max change #iterations 4.171495 177.9979 at 10iterations 1.954337 64.31247 at 20iterations 0.9133057 32.66008 at 30iterations 0.4250602 13.96939 at 40iterations 0.1987526 6.879578 at 50iterations 9.2950650E-02 2.873585 at 60iterations 4.3335427E-02 1.391146 at 70iterations 2.0301012E-02 0.7368202 at 80iterations 9.4898473E-03 0.2832642 at 90iterations 4.4353716E-03 0.1471229 at 100iterations 2.0687340E-03 6.6459656E-02 at 110iterations 9.6524996E-04 3.0405045E-02 at 120iterations finished qdiffx linear iterations at : 22:11:54 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 9.6524996E-04 3.0405045E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 22:11:54 7.886u 0.198s 0:08.40 96.0% 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 Sun Oct 9 2011 at 22:11:54 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 = 2576 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.859285 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): -9.044000 45.88100 ymin,ymax (A): -16.49500 39.53300 zmin,zma (A): -3.814000 49.19000 x,y,z range (A): 54.92500 56.02800 53.00400 scale (grids/A): 2.859285 object centre (A): 18.41850 11.51900 22.68800 number of atom coordinates read : 2576 total number of charged atoms : 2432 net assigned charge : 5.000012 assigned positive charge : 388.4979 centred at (gu) : 95.27513 90.80824 90.97839 assigned negative charge : -383.4987 centred at (gu) : 95.56102 90.67723 91.06203 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 170754 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22117 grid for indexing accessible points = 1.400000 m= 81536 mr = 122721 m= 26697 mr = 65957 m= 6293 mr = 20861 m= 1011 mr = 4619 m= 65 mr = 765 m= 0 mr = 25 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 8008 time to turn everything in is 0.9500000 number of dielectric boundary points 71408 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 19454 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) : 1.906190 object centre at (A) : 18.41850 11.51900 22.68800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4205073 -0.2470004 midg,1,midg; midg,igrid,midg 0.2109330 4.9000010E-02 1,midg,midg; igrid,midg,midg -0.2174858 0.2495877 gauss-seidel spectral radius is 0.9992575 estimated iterations to convergence 290 setup time was (sec) 1.170000 now iterating at: 22:11:56 rms-change max change #iterations 9.828049 336.9073 at 10iterations 5.709489 114.7818 at 20iterations 3.291283 65.98946 at 30iterations 1.896591 38.22363 at 40iterations 1.090215 21.34951 at 50iterations 0.6257055 11.76044 at 60iterations 0.3586816 6.722460 at 70iterations 0.2059114 3.809721 at 80iterations 0.1180779 2.204527 at 90iterations 6.7634694E-02 1.189934 at 100iterations 3.8793236E-02 0.6676240 at 110iterations 2.2225711E-02 0.4297333 at 120iterations 1.2747898E-02 0.2724495 at 130iterations 7.3019713E-03 0.1277962 at 140iterations 4.1840975E-03 7.5918913E-02 at 150iterations 2.3996243E-03 4.1564941E-02 at 160iterations 1.3740574E-03 2.4577141E-02 at 170iterations 7.8836892E-04 1.5799046E-02 at 180iterations finished qdiffx linear iterations at : 22:12:07 total time elapsed so far: 12.52000 # loops : 180 mean,max change (kT/e) : 7.8836892E-04 1.5799046E-02 energy calculations done at 12.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.65000 DelPhi exited at 22:12:07 12.654u 0.216s 0:13.18 97.5% 0+0k 0+0io 0pf+0w