Mon Oct 10 00:34:00 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 Mon Oct 10 2011 at 00:34:00 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2989 !!! WARNING: HIY 166 has a net charge of 0.2000 !!! WARNING: ZN1 1086 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6131799 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): 9.412999 67.47100 ymin,ymax (A): -37.19700 11.69800 zmin,zma (A): -22.95900 29.13800 x,y,z range (A): 58.05800 48.89500 52.09700 scale (grids/A): 0.6131799 object centre (A): 38.44200 -12.74950 3.089500 number of atom coordinates read : 2989 total number of charged atoms : 2851 net assigned charge : -10.39998 assigned positive charge : 439.9315 centred at (gu) : 89.51588 89.64756 91.58327 assigned negative charge : -450.3321 centred at (gu) : 89.39265 89.85441 91.76180 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7389 nv = 96 ne = 84 npr = 62513 no. pairs analyzed = 62513 no. exposed pairs = 3593 no. arc points = 24777 no. surface atoms = 1216 nbur = 1773 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 366 mr = 4140 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3500000 number of dielectric boundary points 3572 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2458 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9279 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0443694E-09 -2.5697711E-08 midg,1,midg; midg,igrid,midg 6.7160322E-09 -1.8366872E-08 1,midg,midg; igrid,midg,midg -1.6037529E-08 9.5544339E-10 gauss-seidel spectral radius is 0.9862610 estimated iterations to convergence 70 setup time was (sec) 0.6100000 now iterating at: 00:34:00 rms-change max change #iterations 0.1311030 20.83928 at 10iterations 1.2239547E-02 1.913589 at 20iterations 1.2660576E-03 0.2679138 at 30iterations 3.0477857E-04 6.4405441E-02 at 40iterations 1.2312447E-04 2.5550842E-02 at 50iterations finished qdiffx linear iterations at : 00:34:03 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 1.2312447E-04 2.5550842E-02 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 00:34:04 3.661u 0.199s 0:04.13 93.2% 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 Mon Oct 10 2011 at 00:34:04 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2989 !!! WARNING: HIY 166 has a net charge of 0.2000 !!! WARNING: ZN1 1086 has a net charge of 1.4000 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: 1.839540 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): 9.412999 67.47100 ymin,ymax (A): -37.19700 11.69800 zmin,zma (A): -22.95900 29.13800 x,y,z range (A): 58.05800 48.89500 52.09700 scale (grids/A): 1.839540 object centre (A): 38.44200 -12.74950 3.089500 number of atom coordinates read : 2989 total number of charged atoms : 2851 net assigned charge : -10.39998 assigned positive charge : 439.9315 centred at (gu) : 88.54696 88.94214 94.74924 assigned negative charge : -450.3321 centred at (gu) : 88.17764 89.56275 95.28506 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 80970 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24777 grid for indexing accessible points = 1.400000 m= 28718 mr = 57221 m= 4342 mr = 20990 m= 252 mr = 2623 m= 1 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1555 time to turn everything in is 0.6300000 number of dielectric boundary points 33360 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 188 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 22362 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) : 0.6131799 object centre at (A) : 38.44200 -12.74950 3.089500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2860798E-02 -6.1524708E-02 midg,1,midg; midg,igrid,midg 5.1453593E-03 -2.2651747E-02 1,midg,midg; igrid,midg,midg -4.2199928E-02 -2.4840403E-02 gauss-seidel spectral radius is 0.9985743 estimated iterations to convergence 210 setup time was (sec) 0.9600000 now iterating at: 00:34:05 rms-change max change #iterations 4.244750 157.6637 at 10iterations 1.951794 60.10220 at 20iterations 0.9027322 28.19268 at 30iterations 0.4147194 12.07667 at 40iterations 0.1907968 6.670509 at 50iterations 8.7925546E-02 2.689470 at 60iterations 4.0506840E-02 1.409225 at 70iterations 1.8777873E-02 0.6121295 at 80iterations 8.6680725E-03 0.2536621 at 90iterations 4.0329248E-03 0.1225834 at 100iterations 1.8944753E-03 5.5982590E-02 at 110iterations 9.1330131E-04 3.0250549E-02 at 120iterations finished qdiffx linear iterations at : 00:34:12 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 9.1330131E-04 3.0250549E-02 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.160000 DelPhi exited at 00:34:13 8.165u 0.223s 0:08.71 96.2% 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 Mon Oct 10 2011 at 00:34:13 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2989 !!! WARNING: HIY 166 has a net charge of 0.2000 !!! WARNING: ZN1 1086 has a net charge of 1.4000 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: 2.759310 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): 9.412999 67.47100 ymin,ymax (A): -37.19700 11.69800 zmin,zma (A): -22.95900 29.13800 x,y,z range (A): 58.05800 48.89500 52.09700 scale (grids/A): 2.759310 object centre (A): 38.44200 -12.74950 3.089500 number of atom coordinates read : 2989 total number of charged atoms : 2851 net assigned charge : -10.39998 assigned positive charge : 439.9315 centred at (gu) : 87.82028 88.41303 97.12397 assigned negative charge : -450.3321 centred at (gu) : 87.26632 89.34411 97.92763 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 187508 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24777 grid for indexing accessible points = 1.400000 m= 94011 mr = 138642 m= 33246 mr = 77105 m= 7599 mr = 26298 m= 1053 mr = 5534 m= 56 mr = 696 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 5135 time to turn everything in is 1.560000 number of dielectric boundary points 75177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 22807 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) : 1.839540 object centre at (A) : 38.44200 -12.74950 3.089500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3646018 -0.6889705 midg,1,midg; midg,igrid,midg 5.8801681E-02 -0.1266009 1,midg,midg; igrid,midg,midg -0.4160343 -0.3713973 gauss-seidel spectral radius is 0.9992443 estimated iterations to convergence 287 setup time was (sec) 1.920000 now iterating at: 00:34:15 rms-change max change #iterations 10.09424 310.0321 at 10iterations 5.873756 120.9975 at 20iterations 3.390912 66.45241 at 30iterations 1.954728 39.40762 at 40iterations 1.122387 21.76853 at 50iterations 0.6449569 12.70981 at 60iterations 0.3697735 6.833118 at 70iterations 0.2121576 3.873169 at 80iterations 0.1215329 2.343190 at 90iterations 6.9449529E-02 1.208398 at 100iterations 3.9745566E-02 0.7666121 at 110iterations 2.2735398E-02 0.3866711 at 120iterations 1.3043647E-02 0.2264900 at 130iterations 7.4735191E-03 0.1371409 at 140iterations 4.2777201E-03 7.4394226E-02 at 150iterations 2.4492666E-03 4.1213751E-02 at 160iterations 1.4031328E-03 2.4040222E-02 at 170iterations 8.1015489E-04 1.3265610E-02 at 180iterations finished qdiffx linear iterations at : 00:34:26 total time elapsed so far: 12.83000 # loops : 180 mean,max change (kT/e) : 8.1015489E-04 1.3265610E-02 energy calculations done at 12.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.03000 DelPhi exited at 00:34:26 13.036u 0.230s 0:13.62 97.3% 0+0k 0+0io 0pf+0w