Sun Oct 9 13:35:14 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 13:35:15 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 = 2348 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.7110330 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): -18.42600 30.23100 ymin,ymax (A): -20.54900 29.51900 zmin,zma (A): 4.554000 48.36100 x,y,z range (A): 48.65700 50.06800 43.80700 scale (grids/A): 0.7110330 object centre (A): 5.902501 4.485001 26.45750 number of atom coordinates read : 2348 total number of charged atoms : 2208 net assigned charge : 3.500011 assigned positive charge : 355.6151 centred at (gu) : 90.69579 90.30795 90.25945 assigned negative charge : -352.1156 centred at (gu) : 90.74619 90.47491 90.38064 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8131 nv = 96 ne = 84 npr = 47496 no. pairs analyzed = 47496 no. exposed pairs = 2932 no. arc points = 20406 no. surface atoms = 995 nbur = 1353 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 517 mr = 4561 m= 2 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 4002 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1925 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8988 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0021659E-07 -4.3317470E-08 midg,1,midg; midg,igrid,midg 1.2455837E-07 -7.4021749E-08 1,midg,midg; igrid,midg,midg 5.5447099E-08 2.5272509E-09 gauss-seidel spectral radius is 0.9897202 estimated iterations to convergence 80 setup time was (sec) 0.5100000 now iterating at: 13:35:15 rms-change max change #iterations 0.2191596 27.16402 at 10iterations 2.7119758E-02 3.736431 at 20iterations 3.5257561E-03 0.4331474 at 30iterations 5.1875063E-04 6.3297272E-02 at 40iterations 1.0027619E-04 1.3336182E-02 at 50iterations finished qdiffx linear iterations at : 13:35:18 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 1.0027619E-04 1.3336182E-02 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 13:35:18 3.082u 0.160s 0:03.76 86.1% 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 13:35:18 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 = 2348 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.133099 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): -18.42600 30.23100 ymin,ymax (A): -20.54900 29.51900 zmin,zma (A): 4.554000 48.36100 x,y,z range (A): 48.65700 50.06800 43.80700 scale (grids/A): 2.133099 object centre (A): 5.902501 4.485001 26.45750 number of atom coordinates read : 2348 total number of charged atoms : 2208 net assigned charge : 3.500011 assigned positive charge : 355.6151 centred at (gu) : 92.08675 90.92337 90.77792 assigned negative charge : -352.1156 centred at (gu) : 92.23851 91.42450 91.14167 start vw surface at 0.2100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 86345 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20406 grid for indexing accessible points = 1.400000 m= 33283 mr = 60210 m= 6317 mr = 25026 m= 624 mr = 4186 m= 17 mr = 324 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 282 time to turn everything in is 0.6600000 number of dielectric boundary points 36838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 17561 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) : 0.7110330 object centre at (A) : 5.902501 4.485001 26.45750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6345861E-02 9.5552523E-03 midg,1,midg; midg,igrid,midg -1.3519443E-02 -0.1055068 1,midg,midg; igrid,midg,midg -1.0364124E-03 1.1953845E-02 gauss-seidel spectral radius is 0.9988766 estimated iterations to convergence 236 setup time was (sec) 0.9200000 now iterating at: 13:35:19 rms-change max change #iterations 4.984957 186.0644 at 10iterations 2.494881 81.38062 at 20iterations 1.252835 38.27460 at 30iterations 0.6300884 17.94056 at 40iterations 0.3165772 8.419853 at 50iterations 0.1588273 4.679133 at 60iterations 8.0168866E-02 2.239845 at 70iterations 4.0153701E-02 1.160469 at 80iterations 2.0285858E-02 0.6034686 at 90iterations 1.0239337E-02 0.3133488 at 100iterations 5.1785763E-03 0.1480188 at 110iterations 2.6223205E-03 7.3974252E-02 at 120iterations finished qdiffx linear iterations at : 13:35:25 total time elapsed so far: 6.880000 # loops : 120 mean,max change (kT/e) : 2.6223205E-03 7.3974252E-02 energy calculations done at 6.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.050000 DelPhi exited at 13:35:26 7.054u 0.176s 0:07.63 94.6% 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 13:35:26 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 = 2348 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.199648 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): -18.42600 30.23100 ymin,ymax (A): -20.54900 29.51900 zmin,zma (A): 4.554000 48.36100 x,y,z range (A): 48.65700 50.06800 43.80700 scale (grids/A): 3.199648 object centre (A): 5.902501 4.485001 26.45750 number of atom coordinates read : 2348 total number of charged atoms : 2208 net assigned charge : 3.500011 assigned positive charge : 355.6151 centred at (gu) : 93.13007 91.38511 91.16673 assigned negative charge : -352.1156 centred at (gu) : 93.35761 92.13673 91.71249 start vw surface at 0.1600000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 199020 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20406 grid for indexing accessible points = 1.400000 m= 104697 mr = 145196 m= 41196 mr = 86489 m= 11837 mr = 33705 m= 2672 mr = 9183 m= 321 mr = 2034 m= 16 mr = 180 m= 0 mr = 3 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 1047 time to turn everything in is 1.900000 number of dielectric boundary points 82969 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 17664 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) : 2.133099 object centre at (A) : 5.902501 4.485001 26.45750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4953032 4.0267028E-02 midg,1,midg; midg,igrid,midg -0.5278488 -1.219704 1,midg,midg; igrid,midg,midg -8.6817317E-02 1.6156884E-02 gauss-seidel spectral radius is 0.9993120 estimated iterations to convergence 301 setup time was (sec) 2.180000 now iterating at: 13:35:28 rms-change max change #iterations 11.09408 398.0175 at 10iterations 6.648124 132.2952 at 20iterations 3.953264 75.89637 at 30iterations 2.350433 44.60699 at 40iterations 1.392538 23.01727 at 50iterations 0.8273329 14.58269 at 60iterations 0.4878566 7.794252 at 70iterations 0.2884155 5.019287 at 80iterations 0.1703164 2.863068 at 90iterations 0.1002365 1.748463 at 100iterations 5.9205126E-02 1.006203 at 110iterations 3.4871146E-02 0.5851173 at 120iterations 2.0617235E-02 0.3936653 at 130iterations 1.2248174E-02 0.2131710 at 140iterations 7.3258914E-03 0.1206207 at 150iterations 4.4297040E-03 7.2822571E-02 at 160iterations 2.7425182E-03 4.8786163E-02 at 170iterations 1.7642459E-03 3.3851624E-02 at 180iterations finished qdiffx linear iterations at : 13:35:38 total time elapsed so far: 11.71000 # loops : 180 mean,max change (kT/e) : 1.7642459E-03 3.3851624E-02 energy calculations done at 11.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.88000 DelPhi exited at 13:35:38 11.880u 0.183s 0:12.34 97.7% 0+0k 0+0io 0pf+0w