Tue Oct 11 06:58:25 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 Tue Oct 11 2011 at 06:58:25 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2950 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 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: 0.5346389 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): -19.73800 46.84900 ymin,ymax (A): 21.48200 79.21200 zmin,zma (A): -72.41000 -23.36600 x,y,z range (A): 66.58700 57.73000 49.04400 scale (grids/A): 0.5346389 object centre (A): 13.55550 50.34700 -47.88800 number of atom coordinates read : 2950 total number of charged atoms : 2808 net assigned charge : -1.960990 assigned positive charge : 432.4175 centred at (gu) : 88.94118 89.59302 90.09094 assigned negative charge : -434.3792 centred at (gu) : 88.93465 89.68170 90.11545 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5464 nv = 96 ne = 84 npr = 59917 no. pairs analyzed = 59917 no. exposed pairs = 3795 no. arc points = 26991 no. surface atoms = 1275 nbur = 1675 mkacc time = 0.1400000 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= 250 mr = 2791 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 2914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2701 ## 354 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7232 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3516057E-11 -1.8629615E-10 midg,1,midg; midg,igrid,midg 3.2275854E-10 -4.1125608E-10 1,midg,midg; igrid,midg,midg -1.3830875E-10 -3.9776415E-11 gauss-seidel spectral radius is 0.9819744 estimated iterations to convergence 61 setup time was (sec) 0.5700000 now iterating at: 06:58:26 rms-change max change #iterations 6.4580396E-02 11.45796 at 10iterations 4.1544810E-03 0.7284660 at 20iterations 2.7331198E-04 5.3932190E-02 at 30iterations 2.4122628E-05 5.3348541E-03 at 40iterations 3.3350614E-06 8.7165833E-04 at 50iterations finished qdiffx linear iterations at : 06:58:28 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 3.3350614E-06 8.7165833E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 06:58:29 3.472u 0.179s 0:04.12 88.3% 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 Tue Oct 11 2011 at 06:58:29 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2950 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 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: 1.603917 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): -19.73800 46.84900 ymin,ymax (A): 21.48200 79.21200 zmin,zma (A): -72.41000 -23.36600 x,y,z range (A): 66.58700 57.73000 49.04400 scale (grids/A): 1.603917 object centre (A): 13.55550 50.34700 -47.88800 number of atom coordinates read : 2950 total number of charged atoms : 2808 net assigned charge : -1.960990 assigned positive charge : 432.4175 centred at (gu) : 86.82314 88.77836 90.27204 assigned negative charge : -434.3792 centred at (gu) : 86.80344 89.04467 90.34599 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 60601 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26991 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 19243 mr = 40226 m= 2120 mr = 13536 m= 43 mr = 1119 m= 0 mr = 1 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 27125 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 283 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 21397 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) : 0.5346389 object centre at (A) : 13.55550 50.34700 -47.88800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7602219E-03 6.6634100E-03 midg,1,midg; midg,igrid,midg -2.3571777E-03 5.0332360E-03 1,midg,midg; igrid,midg,midg -2.7761247E-04 -2.2888038E-02 gauss-seidel spectral radius is 0.9981228 estimated iterations to convergence 183 setup time was (sec) 0.8100000 now iterating at: 06:58:30 rms-change max change #iterations 3.144345 155.2450 at 10iterations 1.287679 58.63343 at 20iterations 0.5276081 27.57286 at 30iterations 0.2170250 8.368824 at 40iterations 8.9432903E-02 3.371260 at 50iterations 3.6621425E-02 1.352974 at 60iterations 1.5066813E-02 0.5823956 at 70iterations 6.2224097E-03 0.2435417 at 80iterations 2.5536520E-03 9.4061375E-02 at 90iterations 1.0540173E-03 3.8967133E-02 at 100iterations 4.3563067E-04 1.5569687E-02 at 110iterations 1.8105502E-04 7.4062347E-03 at 120iterations finished qdiffx linear iterations at : 06:58:37 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 1.8105502E-04 7.4062347E-03 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 06:58:38 7.904u 0.184s 0:08.53 94.7% 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 Tue Oct 11 2011 at 06:58:38 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2950 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 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: 2.405875 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): -19.73800 46.84900 ymin,ymax (A): 21.48200 79.21200 zmin,zma (A): -72.41000 -23.36600 x,y,z range (A): 66.58700 57.73000 49.04400 scale (grids/A): 2.405875 object centre (A): 13.55550 50.34700 -47.88800 number of atom coordinates read : 2950 total number of charged atoms : 2808 net assigned charge : -1.960990 assigned positive charge : 432.4175 centred at (gu) : 85.23463 88.16724 90.40810 assigned negative charge : -434.3792 centred at (gu) : 85.20499 88.56686 90.51894 start vw surface at 0.1500000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 140659 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26991 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 65743 mr = 98706 m= 19803 mr = 52169 m= 3256 mr = 15361 m= 183 mr = 2259 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.130000 number of dielectric boundary points 61081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 22438 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) : 1.603917 object centre at (A) : 13.55550 50.34700 -47.88800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2153051E-02 0.1254786 midg,1,midg; midg,igrid,midg -6.6910580E-02 0.1142468 1,midg,midg; igrid,midg,midg -4.8019979E-02 -0.6794796 gauss-seidel spectral radius is 0.9991241 estimated iterations to convergence 267 setup time was (sec) 1.460000 now iterating at: 06:58:39 rms-change max change #iterations 8.199583 300.8824 at 10iterations 4.562893 123.0681 at 20iterations 2.530169 56.95998 at 30iterations 1.396437 31.49382 at 40iterations 0.7701189 17.62914 at 50iterations 0.4239303 12.11108 at 60iterations 0.2324763 5.396450 at 70iterations 0.1274931 2.828049 at 80iterations 6.9787204E-02 1.529488 at 90iterations 3.8260631E-02 0.8483985 at 100iterations 2.0970469E-02 0.5132184 at 110iterations 1.1455193E-02 0.2379608 at 120iterations 6.2631136E-03 0.1396427 at 130iterations 3.4271053E-03 7.2319984E-02 at 140iterations 1.8684226E-03 4.2517662E-02 at 150iterations 1.0219645E-03 2.2789478E-02 at 160iterations 5.5808772E-04 1.2661934E-02 at 170iterations 3.0501894E-04 6.4787865E-03 at 180iterations finished qdiffx linear iterations at : 06:58:51 total time elapsed so far: 13.37000 # loops : 180 mean,max change (kT/e) : 3.0501894E-04 6.4787865E-03 energy calculations done at 13.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.56000 DelPhi exited at 06:58:52 13.562u 0.223s 0:14.06 98.0% 0+0k 0+0io 0pf+0w