Sun Oct 9 14:21:21 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 14:21:21 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 = 2724 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: 0.5492725 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): -2.320000 51.16100 ymin,ymax (A): -9.979000 38.24400 zmin,zma (A): -17.12400 47.68900 x,y,z range (A): 53.48100 48.22300 64.81300 scale (grids/A): 0.5492725 object centre (A): 24.42050 14.13250 15.28250 number of atom coordinates read : 2724 total number of charged atoms : 2585 net assigned charge : 5.000011 assigned positive charge : 413.1373 centred at (gu) : 89.87689 91.20654 89.17606 assigned negative charge : -408.1384 centred at (gu) : 89.78482 91.09921 89.25318 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5281 nv = 96 ne = 84 npr = 54636 no. pairs analyzed = 54636 no. exposed pairs = 3550 no. arc points = 25108 no. surface atoms = 1189 nbur = 1535 mkacc time = 0.1200000 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= 225 mr = 2614 m= 0 mr = 5 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2887 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2571 ## 367 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 6949 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0612361E-09 -1.5687865E-10 midg,1,midg; midg,igrid,midg -2.9921332E-10 1.4427912E-09 1,midg,midg; igrid,midg,midg -3.1125866E-10 9.3788255E-10 gauss-seidel spectral radius is 0.9828880 estimated iterations to convergence 63 setup time was (sec) 0.5200000 now iterating at: 14:21:22 rms-change max change #iterations 7.1262300E-02 10.89919 at 10iterations 4.8034126E-03 0.8940353 at 20iterations 3.3037053E-04 5.6493759E-02 at 30iterations 2.8752687E-05 5.0697327E-03 at 40iterations 5.6256004E-06 1.3070107E-03 at 50iterations finished qdiffx linear iterations at : 14:21:24 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 5.6256004E-06 1.3070107E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 14:21:25 3.162u 0.140s 0:03.59 91.9% 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 Sun Oct 9 2011 at 14:21:25 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 = 2724 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: 1.647817 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): -2.320000 51.16100 ymin,ymax (A): -9.979000 38.24400 zmin,zma (A): -17.12400 47.68900 x,y,z range (A): 53.48100 48.22300 64.81300 scale (grids/A): 1.647817 object centre (A): 24.42050 14.13250 15.28250 number of atom coordinates read : 2724 total number of charged atoms : 2585 net assigned charge : 5.000011 assigned positive charge : 413.1373 centred at (gu) : 89.63000 93.61914 87.52757 assigned negative charge : -408.1384 centred at (gu) : 89.35445 93.29727 87.75943 start vw surface at 0.1500000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 58599 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25108 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 17680 mr = 39026 m= 1829 mr = 11587 m= 47 mr = 759 m= 0 mr = 4 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 62 time to turn everything in is 0.4300000 number of dielectric boundary points 26779 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 329 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 19854 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) : 0.5492725 object centre at (A) : 24.42050 14.13250 15.28250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1879229E-02 6.9702459E-03 midg,1,midg; midg,igrid,midg 1.0167338E-03 5.9701055E-03 1,midg,midg; igrid,midg,midg -2.0452280E-02 2.8439043E-03 gauss-seidel spectral radius is 0.9981956 estimated iterations to convergence 187 setup time was (sec) 0.6900000 now iterating at: 14:21:26 rms-change max change #iterations 3.230808 163.4230 at 10iterations 1.346639 59.72911 at 20iterations 0.5593002 21.48097 at 30iterations 0.2333865 8.446801 at 40iterations 9.7183004E-02 3.533823 at 50iterations 4.0606864E-02 1.643654 at 60iterations 1.7041447E-02 0.6433084 at 70iterations 7.1132556E-03 0.2687569 at 80iterations 2.9907441E-03 0.1113813 at 90iterations 1.2474819E-03 4.5676231E-02 at 100iterations 5.2229693E-04 2.1022797E-02 at 110iterations 2.1896756E-04 8.6975098E-03 at 120iterations finished qdiffx linear iterations at : 14:21:32 total time elapsed so far: 6.600000 # loops : 120 mean,max change (kT/e) : 2.1896756E-04 8.6975098E-03 energy calculations done at 6.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.770000 DelPhi exited at 14:21:32 6.775u 0.165s 0:07.24 95.7% 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 14:21:32 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 = 2724 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: 2.471726 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): -2.320000 51.16100 ymin,ymax (A): -9.979000 38.24400 zmin,zma (A): -17.12400 47.68900 x,y,z range (A): 53.48100 48.22300 64.81300 scale (grids/A): 2.471726 object centre (A): 24.42050 14.13250 15.28250 number of atom coordinates read : 2724 total number of charged atoms : 2585 net assigned charge : 5.000011 assigned positive charge : 413.1373 centred at (gu) : 89.44481 95.42857 86.29122 assigned negative charge : -408.1384 centred at (gu) : 89.03160 94.94582 86.63902 start vw surface at 0.1500000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 135907 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25108 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 61500 mr = 95671 m= 17216 mr = 47579 m= 2797 mr = 12265 m= 226 mr = 1683 m= 4 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.5500001 no. cavity mid-points inaccessible to solvent = 237 time to turn everything in is 0.9800000 number of dielectric boundary points 60367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 20654 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) : 1.647817 object centre at (A) : 24.42050 14.13250 15.28250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7818379 0.1461480 midg,1,midg; midg,igrid,midg 2.0980904E-02 2.6270710E-02 1,midg,midg; igrid,midg,midg -0.3568395 4.4321556E-02 gauss-seidel spectral radius is 0.9991345 estimated iterations to convergence 269 setup time was (sec) 1.260000 now iterating at: 14:21:34 rms-change max change #iterations 8.425293 338.5841 at 10iterations 4.790680 145.5690 at 20iterations 2.699539 67.68595 at 30iterations 1.513424 45.54250 at 40iterations 0.8426311 20.44959 at 50iterations 0.4694678 12.16165 at 60iterations 0.2608469 6.174435 at 70iterations 0.1439333 3.369802 at 80iterations 7.9551131E-02 1.818787 at 90iterations 4.3801319E-02 1.192028 at 100iterations 2.4169387E-02 0.5181046 at 110iterations 1.3303860E-02 0.2721000 at 120iterations 7.3316460E-03 0.1635609 at 130iterations 4.0241294E-03 9.5489502E-02 at 140iterations 2.2134664E-03 5.1271439E-02 at 150iterations 1.2183473E-03 2.5453568E-02 at 160iterations 6.7214010E-04 1.4961243E-02 at 170iterations 3.7023725E-04 8.2597733E-03 at 180iterations finished qdiffx linear iterations at : 14:21:43 total time elapsed so far: 10.42000 # loops : 180 mean,max change (kT/e) : 3.7023725E-04 8.2597733E-03 energy calculations done at 10.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.60000 DelPhi exited at 14:21:43 10.604u 0.171s 0:11.08 97.2% 0+0k 0+0io 0pf+0w