Sun Oct 9 03:16:06 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 03:16:06 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4559 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 2 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5332695 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): -4.088000 59.34800 ymin,ymax (A): 0.7229999 67.48100 zmin,zma (A): 169.0660 229.2200 x,y,z range (A): 63.43600 66.75800 60.15401 scale (grids/A): 0.5332695 object centre (A): 27.63000 34.10200 199.1430 number of atom coordinates read : 4559 total number of charged atoms : 4326 net assigned charge : 19.99999 assigned positive charge : 667.1890 centred at (gu) : 90.11852 91.25356 88.30379 assigned negative charge : -647.1937 centred at (gu) : 90.11178 91.23049 88.32858 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8220 nv = 96 ne = 84 npr = 94601 no. pairs analyzed = 94601 no. exposed pairs = 5817 no. arc points = 39660 no. surface atoms = 1952 nbur = 2607 mkacc time = 0.1600000 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 = 1.596000 m= 330 mr = 4285 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4254 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3908 ## 477 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 10872 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3533658E-09 3.9425110E-10 midg,1,midg; midg,igrid,midg 4.4556625E-10 1.1966378E-09 1,midg,midg; igrid,midg,midg 6.7967848E-10 8.0253915E-10 gauss-seidel spectral radius is 0.9819936 estimated iterations to convergence 61 setup time was (sec) 0.4900000 now iterating at: 03:16:07 rms-change max change #iterations 8.2811892E-02 12.38564 at 10iterations 8.1408601E-03 1.431221 at 20iterations 2.3802968E-03 0.3485603 at 30iterations 9.1883045E-04 0.1395302 at 40iterations 3.6173870E-04 5.5368423E-02 at 50iterations finished qdiffx linear iterations at : 03:16:10 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 3.6173870E-04 5.5368423E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 03:16:10 3.478u 0.175s 0:03.97 91.6% 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 03:16:10 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4559 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 2 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.599808 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): -4.088000 59.34800 ymin,ymax (A): 0.7229999 67.48100 zmin,zma (A): 169.0660 229.2200 x,y,z range (A): 63.43600 66.75800 60.15401 scale (grids/A): 1.599808 object centre (A): 27.63000 34.10200 199.1430 number of atom coordinates read : 4559 total number of charged atoms : 4326 net assigned charge : 19.99999 assigned positive charge : 667.1890 centred at (gu) : 90.35370 93.75909 84.90998 assigned negative charge : -647.1937 centred at (gu) : 90.33495 93.69086 84.98548 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 91946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39660 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 28259 mr = 63171 m= 2967 mr = 19054 m= 81 mr = 1411 m= 0 mr = 7 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1151 time to turn everything in is 0.4500000 number of dielectric boundary points 39610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 436 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 32956 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) : 0.5332695 object centre at (A) : 27.63000 34.10200 199.1430 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4048695E-02 1.8499666E-03 midg,1,midg; midg,igrid,midg 1.9117648E-02 1.3728507E-02 1,midg,midg; igrid,midg,midg 3.3632841E-02 1.2440383E-02 gauss-seidel spectral radius is 0.9982672 estimated iterations to convergence 191 setup time was (sec) 0.6800000 now iterating at: 03:16:11 rms-change max change #iterations 4.014382 177.0773 at 10iterations 1.699772 51.91327 at 20iterations 0.7241359 24.86142 at 30iterations 0.3089874 9.689109 at 40iterations 0.1320809 3.842487 at 50iterations 5.7136010E-02 1.735138 at 60iterations 2.5005920E-02 0.7968273 at 70iterations 1.1457631E-02 0.3781834 at 80iterations 5.7740794E-03 0.1998119 at 90iterations 3.2989278E-03 0.1198940 at 100iterations 2.1135744E-03 7.3923111E-02 at 110iterations 1.4576216E-03 4.7746658E-02 at 120iterations finished qdiffx linear iterations at : 03:16:18 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 1.4576216E-03 4.7746658E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 03:16:19 7.848u 0.181s 0:08.31 96.5% 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 03:16:19 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4559 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 2 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.399713 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): -4.088000 59.34800 ymin,ymax (A): 0.7229999 67.48100 zmin,zma (A): 169.0660 229.2200 x,y,z range (A): 63.43600 66.75800 60.15401 scale (grids/A): 2.399713 object centre (A): 27.63000 34.10200 199.1430 number of atom coordinates read : 4559 total number of charged atoms : 4326 net assigned charge : 19.99999 assigned positive charge : 667.1890 centred at (gu) : 90.53008 95.63798 82.36444 assigned negative charge : -647.1937 centred at (gu) : 90.50231 95.53606 82.47809 start vw surface at 0.1100000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 214053 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39660 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 98373 mr = 155191 m= 27675 mr = 77084 m= 4462 mr = 20273 m= 284 mr = 2813 m= 3 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 4133 time to turn everything in is 1.110000 number of dielectric boundary points 89371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 34543 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) : 1.599808 object centre at (A) : 27.63000 34.10200 199.1430 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2302491 -5.1323250E-02 midg,1,midg; midg,igrid,midg 0.2930862 0.1716393 1,midg,midg; igrid,midg,midg 0.4715882 6.0961343E-02 gauss-seidel spectral radius is 0.9992025 estimated iterations to convergence 280 setup time was (sec) 1.360000 now iterating at: 03:16:20 rms-change max change #iterations 10.41233 306.7897 at 10iterations 6.013374 135.8937 at 20iterations 3.453937 71.82511 at 30iterations 1.975493 38.11639 at 40iterations 1.123426 23.03432 at 50iterations 0.6376665 12.21116 at 60iterations 0.3623274 6.885040 at 70iterations 0.2054120 3.583107 at 80iterations 0.1159422 1.989883 at 90iterations 6.5644577E-02 1.142052 at 100iterations 3.7107281E-02 0.7024422 at 110iterations 2.0965613E-02 0.3626175 at 120iterations 1.1900543E-02 0.2120514 at 130iterations 6.8009505E-03 0.1203632 at 140iterations 3.9331582E-03 7.5622559E-02 at 150iterations 2.3234198E-03 4.0016174E-02 at 160iterations 1.4227938E-03 2.7269363E-02 at 170iterations 9.2340983E-04 1.8712997E-02 at 180iterations finished qdiffx linear iterations at : 03:16:32 total time elapsed so far: 12.97000 # loops : 180 mean,max change (kT/e) : 9.2340983E-04 1.8712997E-02 energy calculations done at 12.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 03:16:32 13.097u 0.220s 0:13.57 98.0% 0+0k 0+0io 0pf+0w