Mon Oct 10 14:06:54 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 14:06:54 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3380 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: 0.5358460 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): -15.03200 41.48700 ymin,ymax (A): -39.44500 26.99200 zmin,zma (A): -17.46700 35.12700 x,y,z range (A): 56.51900 66.43700 52.59400 scale (grids/A): 0.5358460 object centre (A): 13.22750 -6.226501 8.830002 number of atom coordinates read : 3380 total number of charged atoms : 3236 net assigned charge : -0.9999876 assigned positive charge : 509.0435 centred at (gu) : 91.19596 91.92134 90.67424 assigned negative charge : -510.0448 centred at (gu) : 91.15117 91.87034 90.63305 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6231 nv = 96 ne = 84 npr = 69006 no. pairs analyzed = 69006 no. exposed pairs = 4115 no. arc points = 28450 no. surface atoms = 1398 nbur = 1982 mkacc time = 0.1500000 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= 251 mr = 3329 m= 0 mr = 11 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2939 ## 428 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8248 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2317410E-10 1.9001101E-10 midg,1,midg; midg,igrid,midg -1.9474962E-10 3.4598954E-10 1,midg,midg; igrid,midg,midg -2.0956474E-10 2.4281005E-10 gauss-seidel spectral radius is 0.9820766 estimated iterations to convergence 62 setup time was (sec) 0.6000000 now iterating at: 14:06:55 rms-change max change #iterations 6.9939129E-02 11.50447 at 10iterations 4.6316665E-03 0.7165146 at 20iterations 3.3905735E-04 5.8883667E-02 at 30iterations 4.7117526E-05 9.1257095E-03 at 40iterations 1.0100583E-05 2.1400452E-03 at 50iterations finished qdiffx linear iterations at : 14:06:58 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.0100583E-05 2.1400452E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 14:06:58 3.451u 0.186s 0:04.10 88.5% 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 Mon Oct 10 2011 at 14:06:58 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3380 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: 1.607538 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): -15.03200 41.48700 ymin,ymax (A): -39.44500 26.99200 zmin,zma (A): -17.46700 35.12700 x,y,z range (A): 56.51900 66.43700 52.59400 scale (grids/A): 1.607538 object centre (A): 13.22750 -6.226501 8.830002 number of atom coordinates read : 3380 total number of charged atoms : 3236 net assigned charge : -0.9999876 assigned positive charge : 509.0435 centred at (gu) : 93.58699 95.76328 92.02166 assigned negative charge : -510.0448 centred at (gu) : 93.45315 95.61075 91.89877 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69848 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28450 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21970 mr = 48625 m= 2076 mr = 15360 m= 59 mr = 866 m= 0 mr = 3 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 29099 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 364 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 24693 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) : 0.5358460 object centre at (A) : 13.22750 -6.226501 8.830002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2843165E-03 5.2541392E-03 midg,1,midg; midg,igrid,midg 4.3038488E-03 1.2347029E-02 1,midg,midg; igrid,midg,midg -4.4306205E-03 -2.8512070E-03 gauss-seidel spectral radius is 0.9981543 estimated iterations to convergence 185 setup time was (sec) 0.7900000 now iterating at: 14:06:59 rms-change max change #iterations 3.430810 172.8767 at 10iterations 1.421076 63.55272 at 20iterations 0.5887192 22.30157 at 30iterations 0.2439711 9.071996 at 40iterations 0.1008768 3.568585 at 50iterations 4.2036854E-02 1.582550 at 60iterations 1.7424002E-02 0.7083168 at 70iterations 7.2307177E-03 0.2459531 at 80iterations 3.0031675E-03 0.1008530 at 90iterations 1.2499321E-03 4.6463013E-02 at 100iterations 5.2141829E-04 1.6848803E-02 at 110iterations 2.1957992E-04 7.5858831E-03 at 120iterations finished qdiffx linear iterations at : 14:07:06 total time elapsed so far: 7.190000 # loops : 120 mean,max change (kT/e) : 2.1957992E-04 7.5858831E-03 energy calculations done at 7.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.360000 DelPhi exited at 14:07:06 7.367u 0.204s 0:07.90 95.6% 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 Mon Oct 10 2011 at 14:07:07 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.411307 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): -15.03200 41.48700 ymin,ymax (A): -39.44500 26.99200 zmin,zma (A): -17.46700 35.12700 x,y,z range (A): 56.51900 66.43700 52.59400 scale (grids/A): 2.411307 object centre (A): 13.22750 -6.226501 8.830002 number of atom coordinates read : 3380 total number of charged atoms : 3236 net assigned charge : -0.9999876 assigned positive charge : 509.0435 centred at (gu) : 95.38037 98.64455 93.03214 assigned negative charge : -510.0448 centred at (gu) : 95.17963 98.41601 92.84818 start vw surface at 0.1900000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 162406 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28450 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 76972 mr = 119197 m= 21345 mr = 61418 m= 3087 mr = 15909 m= 193 mr = 1807 m= 4 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 65611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 25849 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) : 1.607538 object centre at (A) : 13.22750 -6.226501 8.830002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1163774 8.3329707E-02 midg,1,midg; midg,igrid,midg 9.2236614E-03 0.3933652 1,midg,midg; igrid,midg,midg -4.2383019E-02 -3.8903382E-02 gauss-seidel spectral radius is 0.9991317 estimated iterations to convergence 268 setup time was (sec) 1.480000 now iterating at: 14:07:09 rms-change max change #iterations 9.020540 283.8624 at 10iterations 5.051101 127.7303 at 20iterations 2.820506 68.03103 at 30iterations 1.564388 33.74124 at 40iterations 0.8669673 20.07116 at 50iterations 0.4788549 10.08821 at 60iterations 0.2639793 5.477186 at 70iterations 0.1452459 2.942055 at 80iterations 8.0120876E-02 1.547096 at 90iterations 4.4056170E-02 0.8780837 at 100iterations 2.4210215E-02 0.4907837 at 110iterations 1.3309147E-02 0.2658639 at 120iterations 7.3102866E-03 0.1426888 at 130iterations 4.0196627E-03 7.4716568E-02 at 140iterations 2.2142637E-03 4.1915894E-02 at 150iterations 1.2126517E-03 2.4189234E-02 at 160iterations 6.6881906E-04 1.3782501E-02 at 170iterations 3.7127084E-04 7.7676773E-03 at 180iterations finished qdiffx linear iterations at : 14:07:18 total time elapsed so far: 10.89000 # loops : 180 mean,max change (kT/e) : 3.7127084E-04 7.7676773E-03 energy calculations done at 10.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.06000 DelPhi exited at 14:07:19 11.064u 0.216s 0:11.84 95.1% 0+0k 0+0io 0pf+0w