Mon Oct 10 17:15:24 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 Mon Oct 10 2011 at 17:15:24 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 = 2975 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: 0.5380569 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): -49.12000 17.04400 ymin,ymax (A): -26.47200 17.05500 zmin,zma (A): -5.309000 41.98200 x,y,z range (A): 66.16400 43.52700 47.29100 scale (grids/A): 0.5380569 object centre (A): -16.03800 -4.708500 18.33650 number of atom coordinates read : 2975 total number of charged atoms : 2834 net assigned charge : -1.499976 assigned positive charge : 445.4920 centred at (gu) : 90.41080 89.56626 90.61049 assigned negative charge : -446.9932 centred at (gu) : 90.43166 89.45323 90.74788 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5528 nv = 96 ne = 84 npr = 59514 no. pairs analyzed = 59514 no. exposed pairs = 3947 no. arc points = 27471 no. surface atoms = 1334 nbur = 1641 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 = 1.596000 m= 192 mr = 2727 m= 0 mr = 7 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2779 ## 392 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7342 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2031601E-10 -8.7753838E-10 midg,1,midg; midg,igrid,midg -6.9972422E-10 4.3978121E-10 1,midg,midg; igrid,midg,midg 3.8781613E-11 -1.8058653E-10 gauss-seidel spectral radius is 0.9821988 estimated iterations to convergence 62 setup time was (sec) 0.5200000 now iterating at: 17:15:25 rms-change max change #iterations 6.3996233E-02 12.25195 at 10iterations 4.1456209E-03 0.7257938 at 20iterations 2.6243046E-04 5.2286148E-02 at 30iterations 1.6772761E-05 2.7847290E-03 at 40iterations 1.0918692E-06 1.6522408E-04 at 50iterations finished qdiffx linear iterations at : 17:15:28 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 1.0918692E-06 1.6522408E-04 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 17:15:28 3.607u 0.151s 0:04.08 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 Mon Oct 10 2011 at 17:15:28 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 = 2975 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: 1.614171 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): -49.12000 17.04400 ymin,ymax (A): -26.47200 17.05500 zmin,zma (A): -5.309000 41.98200 x,y,z range (A): 66.16400 43.52700 47.29100 scale (grids/A): 1.614171 object centre (A): -16.03800 -4.708500 18.33650 number of atom coordinates read : 2975 total number of charged atoms : 2834 net assigned charge : -1.499976 assigned positive charge : 445.4920 centred at (gu) : 91.23173 88.69794 91.83018 assigned negative charge : -446.9932 centred at (gu) : 91.29475 88.35932 92.24326 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 61746 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27471 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 17205 mr = 40806 m= 1527 mr = 11256 m= 30 mr = 621 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 502 time to turn everything in is 0.4400000 number of dielectric boundary points 27825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 372 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 21627 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) : 0.5380569 object centre at (A) : -16.03800 -4.708500 18.33650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9965138E-03 -1.4672330E-02 midg,1,midg; midg,igrid,midg -4.6263654E-03 2.6200570E-03 1,midg,midg; igrid,midg,midg -1.9511419E-03 -1.2842044E-02 gauss-seidel spectral radius is 0.9981372 estimated iterations to convergence 184 setup time was (sec) 0.7200000 now iterating at: 17:15:29 rms-change max change #iterations 3.190976 162.0485 at 10iterations 1.312324 49.34180 at 20iterations 0.5394367 20.36026 at 30iterations 0.2222961 8.806584 at 40iterations 9.1377817E-02 3.517781 at 50iterations 3.7628438E-02 1.476611 at 60iterations 1.5463484E-02 0.5785408 at 70iterations 6.3858037E-03 0.2493925 at 80iterations 2.6293686E-03 9.5956802E-02 at 90iterations 1.0809347E-03 3.8073540E-02 at 100iterations 4.4581995E-04 1.8701553E-02 at 110iterations 1.8473681E-04 7.0962906E-03 at 120iterations finished qdiffx linear iterations at : 17:15:36 total time elapsed so far: 7.110000 # loops : 120 mean,max change (kT/e) : 1.8473681E-04 7.0962906E-03 energy calculations done at 7.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.290000 DelPhi exited at 17:15:36 7.289u 0.207s 0:07.78 96.1% 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 17:15:36 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 = 2975 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.421256 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): -49.12000 17.04400 ymin,ymax (A): -26.47200 17.05500 zmin,zma (A): -5.309000 41.98200 x,y,z range (A): 66.16400 43.52700 47.29100 scale (grids/A): 2.421256 object centre (A): -16.03800 -4.708500 18.33650 number of atom coordinates read : 2975 total number of charged atoms : 2834 net assigned charge : -1.499976 assigned positive charge : 445.4920 centred at (gu) : 91.84724 88.04672 92.74502 assigned negative charge : -446.9932 centred at (gu) : 91.94211 87.53909 93.36477 start vw surface at 0.2000000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 143985 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27471 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 61451 mr = 100708 m= 15617 mr = 47214 m= 2160 mr = 11204 m= 99 mr = 1326 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.5699999 no. cavity mid-points inaccessible to solvent = 1574 time to turn everything in is 1.060000 number of dielectric boundary points 62821 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 22644 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) : 1.614171 object centre at (A) : -16.03800 -4.708500 18.33650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1286187E-02 -0.2133750 midg,1,midg; midg,igrid,midg -6.4882420E-02 3.4681667E-02 1,midg,midg; igrid,midg,midg -4.9061537E-02 -0.6246764 gauss-seidel spectral radius is 0.9991241 estimated iterations to convergence 267 setup time was (sec) 1.360000 now iterating at: 17:15:38 rms-change max change #iterations 8.547902 272.8181 at 10iterations 4.796875 151.7383 at 20iterations 2.674206 74.39752 at 30iterations 1.484059 36.00573 at 40iterations 0.8209819 20.07535 at 50iterations 0.4527632 10.09160 at 60iterations 0.2482356 6.553944 at 70iterations 0.1360425 3.353316 at 80iterations 7.4461453E-02 1.627512 at 90iterations 4.0836673E-02 0.8595142 at 100iterations 2.2321910E-02 0.4800873 at 110iterations 1.2236720E-02 0.2516365 at 120iterations 6.6802530E-03 0.1408997 at 130iterations 3.6455307E-03 9.4645500E-02 at 140iterations 1.9982429E-03 4.5063019E-02 at 150iterations 1.0916346E-03 2.1976471E-02 at 160iterations 5.9586315E-04 1.4060020E-02 at 170iterations 3.2583473E-04 7.5941682E-03 at 180iterations finished qdiffx linear iterations at : 17:15:48 total time elapsed so far: 11.85000 # loops : 180 mean,max change (kT/e) : 3.2583473E-04 7.5941682E-03 energy calculations done at 11.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.03000 DelPhi exited at 17:15:49 12.036u 0.215s 0:12.55 97.5% 0+0k 0+0io 0pf+0w