Sun Oct 9 19:56:57 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 19:56:57 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3196 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 0.5750654 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): -11.09200 50.81400 ymin,ymax (A): -12.61000 40.26000 zmin,zma (A): 19.63300 75.93000 x,y,z range (A): 61.90600 52.87000 56.29700 scale (grids/A): 0.5750654 object centre (A): 19.86100 13.82500 47.78150 number of atom coordinates read : 3196 total number of charged atoms : 3053 net assigned charge : 3.740021 assigned positive charge : 493.7648 centred at (gu) : 90.52296 90.00163 87.56062 assigned negative charge : -490.0261 centred at (gu) : 90.42760 90.06340 87.51640 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7135 nv = 96 ne = 84 npr = 62040 no. pairs analyzed = 62040 no. exposed pairs = 4242 no. arc points = 30201 no. surface atoms = 1436 nbur = 1760 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 328 mr = 3610 m= 1 mr = 23 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 0.2300000 number of dielectric boundary points 3831 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2977 ## 326 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8919 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1832757E-10 9.0651225E-10 midg,1,midg; midg,igrid,midg 1.9485584E-09 -5.7391153E-10 1,midg,midg; igrid,midg,midg -1.1193110E-09 2.9700542E-09 gauss-seidel spectral radius is 0.9844188 estimated iterations to convergence 66 setup time was (sec) 0.4300000 now iterating at: 19:56:58 rms-change max change #iterations 9.6513592E-02 15.10755 at 10iterations 7.5592408E-03 1.126324 at 20iterations 5.7611341E-04 8.9790344E-02 at 30iterations 5.7037454E-05 9.0751648E-03 at 40iterations 2.0675698E-05 3.0074120E-03 at 50iterations finished qdiffx linear iterations at : 19:57:01 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 2.0675698E-05 3.0074120E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 19:57:01 3.464u 0.183s 0:03.93 92.6% 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 19:57:01 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3196 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.725196 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): -11.09200 50.81400 ymin,ymax (A): -12.61000 40.26000 zmin,zma (A): 19.63300 75.93000 x,y,z range (A): 61.90600 52.87000 56.29700 scale (grids/A): 1.725196 object centre (A): 19.86100 13.82500 47.78150 number of atom coordinates read : 3196 total number of charged atoms : 3053 net assigned charge : 3.740021 assigned positive charge : 493.7648 centred at (gu) : 91.56824 90.00401 82.68071 assigned negative charge : -490.0261 centred at (gu) : 91.28244 90.18997 82.54875 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 77680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30201 grid for indexing accessible points = 1.400000 m= 26194 mr = 52207 m= 3354 mr = 17773 m= 125 mr = 1657 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 35699 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 249 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 23642 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) : 0.5750654 object centre at (A) : 19.86100 13.82500 47.78150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9321836E-04 6.8201441E-03 midg,1,midg; midg,igrid,midg 1.9097725E-02 -1.0696303E-02 1,midg,midg; igrid,midg,midg -4.3789488E-03 1.7311910E-02 gauss-seidel spectral radius is 0.9984075 estimated iterations to convergence 199 setup time was (sec) 0.6200000 now iterating at: 19:57:02 rms-change max change #iterations 4.006233 169.7312 at 10iterations 1.761956 64.14780 at 20iterations 0.7819560 31.98495 at 30iterations 0.3451178 11.03280 at 40iterations 0.1526913 5.323988 at 50iterations 6.7434840E-02 2.546730 at 60iterations 2.9919557E-02 1.221066 at 70iterations 1.3211887E-02 0.4249191 at 80iterations 5.8316989E-03 0.1928883 at 90iterations 2.5874302E-03 9.0773582E-02 at 100iterations 1.1423681E-03 3.7307739E-02 at 110iterations 5.0459499E-04 2.1522522E-02 at 120iterations finished qdiffx linear iterations at : 19:57:09 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 5.0459499E-04 2.1522522E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 19:57:09 7.932u 0.191s 0:08.38 96.8% 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 19:57:09 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3196 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 2.587794 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): -11.09200 50.81400 ymin,ymax (A): -12.61000 40.26000 zmin,zma (A): 19.63300 75.93000 x,y,z range (A): 61.90600 52.87000 56.29700 scale (grids/A): 2.587794 object centre (A): 19.86100 13.82500 47.78150 number of atom coordinates read : 3196 total number of charged atoms : 3053 net assigned charge : 3.740021 assigned positive charge : 493.7648 centred at (gu) : 92.35213 90.00571 79.02088 assigned negative charge : -490.0261 centred at (gu) : 91.92374 90.28482 78.82304 start vw surface at 0.1100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 180168 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30201 grid for indexing accessible points = 1.400000 m= 86746 mr = 127879 m= 27956 mr = 67754 m= 5448 mr = 20732 m= 563 mr = 3559 m= 27 mr = 326 m= 0 mr = 5 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9800000 number of dielectric boundary points 80653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 24396 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) : 1.725196 object centre at (A) : 19.86100 13.82500 47.78150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2787076E-02 8.1862919E-02 midg,1,midg; midg,igrid,midg 0.2833814 -0.2258590 1,midg,midg; igrid,midg,midg 0.1676966 0.2212049 gauss-seidel spectral radius is 0.9992170 estimated iterations to convergence 282 setup time was (sec) 1.230000 now iterating at: 19:57:11 rms-change max change #iterations 10.24560 300.4680 at 10iterations 6.041499 142.6521 at 20iterations 3.513992 84.94191 at 30iterations 2.028885 48.94830 at 40iterations 1.170953 23.14722 at 50iterations 0.6705450 14.52769 at 60iterations 0.3836655 7.185036 at 70iterations 0.2192059 4.885821 at 80iterations 0.1248550 2.643297 at 90iterations 7.1225993E-02 1.397003 at 100iterations 4.0464848E-02 0.7810268 at 110iterations 2.3047913E-02 0.4765196 at 120iterations 1.3103045E-02 0.2711067 at 130iterations 7.4319346E-03 0.1490936 at 140iterations 4.2471648E-03 8.1436157E-02 at 150iterations 2.4449066E-03 5.1443100E-02 at 160iterations 1.4361824E-03 3.3394814E-02 at 170iterations 8.7659428E-04 2.1344185E-02 at 180iterations finished qdiffx linear iterations at : 19:57:22 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 8.7659428E-04 2.1344185E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 19:57:23 12.753u 0.185s 0:13.20 97.9% 0+0k 0+0io 0pf+0w