Tue Oct 11 03:23:46 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 Tue Oct 11 2011 at 03:23:46 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 = 4233 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: 0.5456106 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): -27.55100 30.90200 ymin,ymax (A): -25.08800 34.80600 zmin,zma (A): -30.89600 34.35200 x,y,z range (A): 58.45300 59.89400 65.24800 scale (grids/A): 0.5456106 object centre (A): 1.675501 4.858999 1.727999 number of atom coordinates read : 4233 total number of charged atoms : 4091 net assigned charge : -1.999953 assigned positive charge : 633.2236 centred at (gu) : 92.10703 90.21374 90.70760 assigned negative charge : -635.2270 centred at (gu) : 92.04749 90.31113 90.70914 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8127 nv = 96 ne = 84 npr = 85270 no. pairs analyzed = 85270 no. exposed pairs = 5527 no. arc points = 39191 no. surface atoms = 1861 nbur = 2372 mkacc time = 0.2300000 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 = 1.568000 m= 339 mr = 4080 m= 5 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 4377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3925 ## 522 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 10702 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.9620583E-11 -1.7436493E-10 midg,1,midg; midg,igrid,midg 7.2329287E-10 -1.1084711E-09 1,midg,midg; igrid,midg,midg -4.1080414E-10 7.2072620E-10 gauss-seidel spectral radius is 0.9827828 estimated iterations to convergence 63 setup time was (sec) 0.8100000 now iterating at: 03:23:48 rms-change max change #iterations 8.8867873E-02 12.89971 at 10iterations 5.9096501E-03 0.8992977 at 20iterations 4.4952441E-04 6.9125175E-02 at 30iterations 5.6551075E-05 1.0871172E-02 at 40iterations 1.2614789E-05 2.6330948E-03 at 50iterations finished qdiffx linear iterations at : 03:23:52 total time elapsed so far: 5.580000 # loops : 50 mean,max change (kT/e) : 1.2614789E-05 2.6330948E-03 energy calculations done at 5.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.750000 DelPhi exited at 03:23:54 5.755u 0.421s 0:07.41 83.2% 0+0k 0+0io 6pf+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 Tue Oct 11 2011 at 03:23:54 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 = 4233 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: 1.636832 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): -27.55100 30.90200 ymin,ymax (A): -25.08800 34.80600 zmin,zma (A): -30.89600 34.35200 x,y,z range (A): 58.45300 59.89400 65.24800 scale (grids/A): 1.636832 object centre (A): 1.675501 4.858999 1.727999 number of atom coordinates read : 4233 total number of charged atoms : 4091 net assigned charge : -1.999953 assigned positive charge : 633.2236 centred at (gu) : 96.31941 90.63990 92.12102 assigned negative charge : -635.2270 centred at (gu) : 96.14178 90.93265 92.12672 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 89992 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39191 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25914 mr = 59711 m= 2531 mr = 17052 m= 63 mr = 1160 m= 0 mr = 6 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7700000 number of dielectric boundary points 40571 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 486 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 31295 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) : 0.5456106 object centre at (A) : 1.675501 4.858999 1.727999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7863300E-02 -3.6613233E-02 midg,1,midg; midg,igrid,midg 1.4143292E-02 -1.4596762E-02 1,midg,midg; igrid,midg,midg 2.4975296E-03 1.9898305E-02 gauss-seidel spectral radius is 0.9983238 estimated iterations to convergence 194 setup time was (sec) 1.180000 now iterating at: 03:23:56 rms-change max change #iterations 4.078803 178.7989 at 10iterations 1.754986 55.22168 at 20iterations 0.7541687 26.74446 at 30iterations 0.3242535 9.782462 at 40iterations 0.1398667 4.691373 at 50iterations 6.0430784E-02 1.748970 at 60iterations 2.5959352E-02 0.8646102 at 70iterations 1.1218350E-02 0.4109859 at 80iterations 4.8596966E-03 0.1431026 at 90iterations 2.0904723E-03 6.8612337E-02 at 100iterations 9.0601563E-04 2.9834747E-02 at 110iterations 3.9357410E-04 1.1875153E-02 at 120iterations finished qdiffx linear iterations at : 03:24:08 total time elapsed so far: 14.12000 # loops : 120 mean,max change (kT/e) : 3.9357410E-04 1.1875153E-02 energy calculations done at 14.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.30000 DelPhi exited at 03:24:09 14.302u 0.472s 0:15.13 97.6% 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 Tue Oct 11 2011 at 03:24:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4233 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: 2.455248 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): -27.55100 30.90200 ymin,ymax (A): -25.08800 34.80600 zmin,zma (A): -30.89600 34.35200 x,y,z range (A): 58.45300 59.89400 65.24800 scale (grids/A): 2.455248 object centre (A): 1.675501 4.858999 1.727999 number of atom coordinates read : 4233 total number of charged atoms : 4091 net assigned charge : -1.999953 assigned positive charge : 633.2236 centred at (gu) : 99.47900 90.95946 93.18122 assigned negative charge : -635.2270 centred at (gu) : 99.21259 91.39881 93.18999 start vw surface at 0.1600000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 209064 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39191 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 91520 mr = 146573 m= 24298 mr = 70755 m= 3920 mr = 17668 m= 290 mr = 2445 m= 3 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.870000 number of dielectric boundary points 91532 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 32692 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) : 1.636832 object centre at (A) : 1.675501 4.858999 1.727999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3028731 -0.8464819 midg,1,midg; midg,igrid,midg 0.1710509 -0.1923494 1,midg,midg; igrid,midg,midg 3.3535291E-02 0.2766911 gauss-seidel spectral radius is 0.9992204 estimated iterations to convergence 283 setup time was (sec) 2.290000 now iterating at: 03:24:12 rms-change max change #iterations 10.63875 444.1985 at 10iterations 6.205679 142.1270 at 20iterations 3.604402 70.86539 at 30iterations 2.076891 44.86897 at 40iterations 1.191620 25.12033 at 50iterations 0.6839613 15.69630 at 60iterations 0.3895740 8.141593 at 70iterations 0.2224685 5.020670 at 80iterations 0.1264287 2.303259 at 90iterations 7.1879633E-02 1.352091 at 100iterations 4.0818453E-02 0.7500556 at 110iterations 2.3180874E-02 0.4198227 at 120iterations 1.3202196E-02 0.2274827 at 130iterations 7.4649355E-03 0.1266994 at 140iterations 4.2346888E-03 7.3793411E-02 at 150iterations 2.4007061E-03 4.1630298E-02 at 160iterations 1.3622673E-03 2.5014877E-02 at 170iterations 7.7336904E-04 1.4080048E-02 at 180iterations finished qdiffx linear iterations at : 03:24:34 total time elapsed so far: 24.06000 # loops : 180 mean,max change (kT/e) : 7.7336904E-04 1.4080048E-02 energy calculations done at 24.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.22000 DelPhi exited at 03:24:34 24.229u 0.510s 0:25.17 98.2% 0+0k 0+0io 0pf+0w