Mon Oct 10 09:46:01 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 09:46:01 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2908 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: 0.5669061 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): 111.9540 174.7510 ymin,ymax (A): -42.41200 10.67500 zmin,zma (A): 49.90700 104.9130 x,y,z range (A): 62.79700 53.08700 55.00600 scale (grids/A): 0.5669061 object centre (A): 143.3525 -15.86850 77.41000 number of atom coordinates read : 2908 total number of charged atoms : 2759 net assigned charge : 8.000018 assigned positive charge : 428.2938 centred at (gu) : 90.32726 88.76433 88.58253 assigned negative charge : -420.2944 centred at (gu) : 90.34159 88.86960 88.46167 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6166 nv = 96 ne = 84 npr = 56248 no. pairs analyzed = 56248 no. exposed pairs = 4637 no. arc points = 33762 no. surface atoms = 1526 nbur = 1382 mkacc time = 0.1700000 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 = 1.512000 m= 335 mr = 2438 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 4058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3300 ## 349 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7943 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.7640289E-10 1.9205133E-09 midg,1,midg; midg,igrid,midg 3.3407110E-09 -2.2272741E-10 1,midg,midg; igrid,midg,midg 1.1969162E-09 9.8181530E-10 gauss-seidel spectral radius is 0.9839621 estimated iterations to convergence 65 setup time was (sec) 0.6500000 now iterating at: 09:46:02 rms-change max change #iterations 8.5614018E-02 15.91316 at 10iterations 6.2908083E-03 0.9798927 at 20iterations 4.7220752E-04 7.6957703E-02 at 30iterations 4.8297366E-05 6.7348480E-03 at 40iterations 8.9668756E-06 1.0118484E-03 at 50iterations finished qdiffx linear iterations at : 09:46:06 total time elapsed so far: 3.920000 # loops : 50 mean,max change (kT/e) : 8.9668756E-06 1.0118484E-03 energy calculations done at 3.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 09:46:06 4.101u 0.266s 0:04.64 93.9% 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 09:46:06 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2908 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: 1.700718 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): 111.9540 174.7510 ymin,ymax (A): -42.41200 10.67500 zmin,zma (A): 49.90700 104.9130 x,y,z range (A): 62.79700 53.08700 55.00600 scale (grids/A): 1.700718 object centre (A): 143.3525 -15.86850 77.41000 number of atom coordinates read : 2908 total number of charged atoms : 2759 net assigned charge : 8.000018 assigned positive charge : 428.2938 centred at (gu) : 90.98120 86.29269 85.74709 assigned negative charge : -420.2944 centred at (gu) : 91.02443 86.60857 85.38496 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 65520 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33762 grid for indexing accessible points = 1.400000 m= 19621 mr = 37691 m= 2603 mr = 11377 m= 112 mr = 1056 m= 3 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 37730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 292 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 21339 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) : 0.5669061 object centre at (A) : 143.3525 -15.86850 77.41000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8028294E-03 1.9612452E-02 midg,1,midg; midg,igrid,midg 2.0352937E-02 5.6088613E-03 1,midg,midg; igrid,midg,midg 9.8813549E-03 1.5100310E-02 gauss-seidel spectral radius is 0.9983552 estimated iterations to convergence 196 setup time was (sec) 0.9200000 now iterating at: 09:46:07 rms-change max change #iterations 3.533963 159.6712 at 10iterations 1.527463 55.13031 at 20iterations 0.6597704 27.13983 at 30iterations 0.2851647 11.90420 at 40iterations 0.1235757 4.444220 at 50iterations 5.3700980E-02 2.107168 at 60iterations 2.3143217E-02 0.8632317 at 70iterations 1.0065865E-02 0.3656297 at 80iterations 4.3714857E-03 0.1674652 at 90iterations 1.8891055E-03 7.0346832E-02 at 100iterations 8.2432816E-04 3.0824661E-02 at 110iterations 3.5605422E-04 1.3809204E-02 at 120iterations finished qdiffx linear iterations at : 09:46:16 total time elapsed so far: 9.200000 # loops : 120 mean,max change (kT/e) : 3.5605422E-04 1.3809204E-02 energy calculations done at 9.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.370000 DelPhi exited at 09:46:16 9.374u 0.305s 0:10.04 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 Mon Oct 10 2011 at 09:46:16 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2908 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: 2.551077 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): 111.9540 174.7510 ymin,ymax (A): -42.41200 10.67500 zmin,zma (A): 49.90700 104.9130 x,y,z range (A): 62.79700 53.08700 55.00600 scale (grids/A): 2.551077 object centre (A): 143.3525 -15.86850 77.41000 number of atom coordinates read : 2908 total number of charged atoms : 2759 net assigned charge : 8.000018 assigned positive charge : 428.2938 centred at (gu) : 91.47176 84.43885 83.62059 assigned negative charge : -420.2944 centred at (gu) : 91.53660 84.91286 83.07734 start vw surface at 0.1800000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 151294 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33762 grid for indexing accessible points = 1.400000 m= 64346 mr = 94051 m= 20192 mr = 45269 m= 4027 mr = 13357 m= 389 mr = 2280 m= 8 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.530000 number of dielectric boundary points 85167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 22064 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) : 1.700718 object centre at (A) : 143.3525 -15.86850 77.41000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1405405 0.2701279 midg,1,midg; midg,igrid,midg 0.2467647 0.1132440 1,midg,midg; igrid,midg,midg 0.1403384 0.2501587 gauss-seidel spectral radius is 0.9992147 estimated iterations to convergence 282 setup time was (sec) 1.850000 now iterating at: 09:46:18 rms-change max change #iterations 9.325703 323.1620 at 10iterations 5.550963 174.0475 at 20iterations 3.242076 80.83984 at 30iterations 1.881949 42.94672 at 40iterations 1.084329 27.02533 at 50iterations 0.6220341 16.24088 at 60iterations 0.3557785 8.898254 at 70iterations 0.2027709 5.021791 at 80iterations 0.1152380 2.823015 at 90iterations 6.5632693E-02 1.663361 at 100iterations 3.7168313E-02 0.9115016 at 110iterations 2.1040596E-02 0.4422550 at 120iterations 1.1918325E-02 0.2486606 at 130iterations 6.7397780E-03 0.1427411 at 140iterations 3.8114383E-03 8.3179474E-02 at 150iterations 2.1533282E-03 4.4096947E-02 at 160iterations 1.2176285E-03 2.7560234E-02 at 170iterations 6.8764453E-04 1.4126778E-02 at 180iterations finished qdiffx linear iterations at : 09:46:32 total time elapsed so far: 15.54000 # loops : 180 mean,max change (kT/e) : 6.8764453E-04 1.4126778E-02 energy calculations done at 15.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.72000 DelPhi exited at 09:46:32 15.721u 0.307s 0:16.33 98.1% 0+0k 0+0io 0pf+0w