Sun Oct 9 14:16:45 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 14:16:45 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2658 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5584401 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): -1.427000 49.28200 ymin,ymax (A): -7.948000 39.40000 zmin,zma (A): -16.05200 47.69700 x,y,z range (A): 50.70900 47.34800 63.74900 scale (grids/A): 0.5584401 object centre (A): 23.92750 15.72600 15.82250 number of atom coordinates read : 2658 total number of charged atoms : 2519 net assigned charge : 7.000018 assigned positive charge : 402.1885 centred at (gu) : 90.16845 90.23795 89.35341 assigned negative charge : -395.1895 centred at (gu) : 90.12999 90.12545 89.36745 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5447 nv = 96 ne = 84 npr = 52324 no. pairs analyzed = 52324 no. exposed pairs = 3428 no. arc points = 24201 no. surface atoms = 1154 nbur = 1504 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 = 1.540000 m= 226 mr = 2774 m= 1 mr = 6 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 0.3100000 number of dielectric boundary points 2894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2458 ## 323 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7018 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.6720310E-10 4.8867788E-10 midg,1,midg; midg,igrid,midg -3.4201858E-10 1.8357472E-09 1,midg,midg; igrid,midg,midg 3.2607170E-10 1.0988691E-09 gauss-seidel spectral radius is 0.9834362 estimated iterations to convergence 64 setup time was (sec) 0.5500000 now iterating at: 14:16:46 rms-change max change #iterations 7.7615850E-02 15.51112 at 10iterations 5.3685498E-03 0.9971428 at 20iterations 4.1606472E-04 6.8019867E-02 at 30iterations 5.0656719E-05 1.0782242E-02 at 40iterations 1.1087473E-05 2.5129318E-03 at 50iterations finished qdiffx linear iterations at : 14:16:48 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.1087473E-05 2.5129318E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 14:16:49 3.331u 0.169s 0:03.77 92.5% 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 14:16:49 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2658 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.675320 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): -1.427000 49.28200 ymin,ymax (A): -7.948000 39.40000 zmin,zma (A): -16.05200 47.69700 x,y,z range (A): 50.70900 47.34800 63.74900 scale (grids/A): 1.675320 object centre (A): 23.92750 15.72600 15.82250 number of atom coordinates read : 2658 total number of charged atoms : 2519 net assigned charge : 7.000018 assigned positive charge : 402.1885 centred at (gu) : 90.50456 90.71306 88.05954 assigned negative charge : -395.1895 centred at (gu) : 90.38977 90.37634 88.10224 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 60331 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24201 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18212 mr = 40621 m= 1810 mr = 12105 m= 68 mr = 765 m= 0 mr = 6 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 26924 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 287 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 19402 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) : 0.5584401 object centre at (A) : 23.92750 15.72600 15.82250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1678812E-02 1.2044105E-02 midg,1,midg; midg,igrid,midg -1.4863005E-04 4.2851674E-03 1,midg,midg; igrid,midg,midg -7.1494714E-03 4.0433630E-03 gauss-seidel spectral radius is 0.9982532 estimated iterations to convergence 190 setup time was (sec) 0.7100000 now iterating at: 14:16:50 rms-change max change #iterations 3.277739 178.3436 at 10iterations 1.394300 53.45396 at 20iterations 0.5876009 22.28647 at 30iterations 0.2504673 9.173958 at 40iterations 0.1057304 3.939753 at 50iterations 4.4866771E-02 1.680809 at 60iterations 1.9023731E-02 0.7248631 at 70iterations 8.0791805E-03 0.3232384 at 80iterations 3.4312303E-03 0.1357989 at 90iterations 1.4568840E-03 5.3573608E-02 at 100iterations 6.2111876E-04 2.6499748E-02 at 110iterations 2.6529859E-04 1.0490417E-02 at 120iterations finished qdiffx linear iterations at : 14:16:57 total time elapsed so far: 8.170000 # loops : 120 mean,max change (kT/e) : 2.6529859E-04 1.0490417E-02 energy calculations done at 8.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.350000 DelPhi exited at 14:16:58 8.353u 0.196s 0:08.86 96.3% 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 14:16:58 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2658 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.512980 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): -1.427000 49.28200 ymin,ymax (A): -7.948000 39.40000 zmin,zma (A): -16.05200 47.69700 x,y,z range (A): 50.70900 47.34800 63.74900 scale (grids/A): 2.512980 object centre (A): 23.92750 15.72600 15.82250 number of atom coordinates read : 2658 total number of charged atoms : 2519 net assigned charge : 7.000018 assigned positive charge : 402.1885 centred at (gu) : 90.75672 91.06945 87.08932 assigned negative charge : -395.1895 centred at (gu) : 90.58474 90.56437 87.15327 start vw surface at 0.1400000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 139989 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24201 grid for indexing accessible points = 1.400000 m= 63254 mr = 99413 m= 17365 mr = 49283 m= 2749 mr = 12507 m= 240 mr = 1649 m= 5 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.010000 number of dielectric boundary points 60661 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 20121 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) : 1.675320 object centre at (A) : 23.92750 15.72600 15.82250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7971494 0.2107022 midg,1,midg; midg,igrid,midg -2.4190515E-03 1.2330756E-02 1,midg,midg; igrid,midg,midg -8.6446509E-02 4.8534524E-02 gauss-seidel spectral radius is 0.9991534 estimated iterations to convergence 271 setup time was (sec) 1.310000 now iterating at: 14:16:59 rms-change max change #iterations 8.530644 282.6504 at 10iterations 4.862217 150.8881 at 20iterations 2.763896 65.76971 at 30iterations 1.555715 38.18563 at 40iterations 0.8716980 21.76114 at 50iterations 0.4880072 11.25338 at 60iterations 0.2724349 5.577305 at 70iterations 0.1513829 3.597475 at 80iterations 8.4153794E-02 1.805916 at 90iterations 4.6728324E-02 1.139664 at 100iterations 2.5919769E-02 0.6188836 at 110iterations 1.4338043E-02 0.2949562 at 120iterations 7.9649575E-03 0.1738770 at 130iterations 4.4039120E-03 0.1007233 at 140iterations 2.4413217E-03 5.5030823E-02 at 150iterations 1.3512590E-03 2.8247356E-02 at 160iterations 7.4936426E-04 1.5933990E-02 at 170iterations 4.1786404E-04 8.6593628E-03 at 180iterations finished qdiffx linear iterations at : 14:17:09 total time elapsed so far: 11.34000 # loops : 180 mean,max change (kT/e) : 4.1786404E-04 8.6593628E-03 energy calculations done at 11.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.51000 DelPhi exited at 14:17:10 11.513u 0.231s 0:12.01 97.7% 0+0k 0+0io 0pf+0w