Mon Oct 10 13:59:27 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 13:59:27 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 = 4697 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5122744 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): -57.19100 7.239000 ymin,ymax (A): -49.96800 7.196000 zmin,zma (A): -73.85300 -4.359000 x,y,z range (A): 64.43000 57.16400 69.49400 scale (grids/A): 0.5122744 object centre (A): -24.97600 -21.38600 -39.10600 number of atom coordinates read : 4697 total number of charged atoms : 4543 net assigned charge : 10.00005 assigned positive charge : 709.5159 centred at (gu) : 90.31425 90.24416 88.81367 assigned negative charge : -699.5207 centred at (gu) : 90.24281 90.34099 88.89250 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7766 nv = 96 ne = 84 npr = 95263 no. pairs analyzed = 95263 no. exposed pairs = 5573 no. arc points = 38580 no. surface atoms = 1893 nbur = 2804 mkacc time = 0.2500000 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 = 1.680000 m= 238 mr = 4146 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 3850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3923 ## 612 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 10474 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9608206E-10 -4.7409066E-11 midg,1,midg; midg,igrid,midg 3.8527379E-10 -1.2571244E-10 1,midg,midg; igrid,midg,midg -4.2283729E-11 3.7252293E-10 gauss-seidel spectral radius is 0.9805027 estimated iterations to convergence 59 setup time was (sec) 0.7600000 now iterating at: 13:59:28 rms-change max change #iterations 7.0452146E-02 11.06033 at 10iterations 5.0420496E-03 0.6649990 at 20iterations 9.6159661E-04 0.1457348 at 30iterations 3.2565653E-04 5.2886963E-02 at 40iterations 1.1769737E-04 1.9546509E-02 at 50iterations finished qdiffx linear iterations at : 13:59:32 total time elapsed so far: 4.730000 # loops : 50 mean,max change (kT/e) : 1.1769737E-04 1.9546509E-02 energy calculations done at 4.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.900000 DelPhi exited at 13:59:33 4.903u 0.406s 0:06.07 87.3% 0+0k 0+0io 6pf+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 13:59:33 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 = 4697 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.536823 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): -57.19100 7.239000 ymin,ymax (A): -49.96800 7.196000 zmin,zma (A): -73.85300 -4.359000 x,y,z range (A): 64.43000 57.16400 69.49400 scale (grids/A): 1.536823 object centre (A): -24.97600 -21.38600 -39.10600 number of atom coordinates read : 4697 total number of charged atoms : 4543 net assigned charge : 10.00005 assigned positive charge : 709.5159 centred at (gu) : 90.94144 90.73117 86.43942 assigned negative charge : -699.5207 centred at (gu) : 90.72807 91.02261 86.67726 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 88596 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38580 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25250 mr = 62021 m= 2038 mr = 17200 m= 52 mr = 913 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 606 time to turn everything in is 0.7100000 number of dielectric boundary points 35802 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 570 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 34132 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) : 0.5122744 object centre at (A) : -24.97600 -21.38600 -39.10600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4802649E-02 -1.0669857E-02 midg,1,midg; midg,igrid,midg 1.2827396E-02 -2.0871875E-03 1,midg,midg; igrid,midg,midg -1.7768944E-03 2.6399136E-02 gauss-seidel spectral radius is 0.9981128 estimated iterations to convergence 183 setup time was (sec) 1.070000 now iterating at: 13:59:35 rms-change max change #iterations 3.735113 151.2425 at 10iterations 1.528266 50.55131 at 20iterations 0.6288891 21.05825 at 30iterations 0.2578165 8.812466 at 40iterations 0.1061863 3.335995 at 50iterations 4.3788310E-02 1.484615 at 60iterations 1.8123886E-02 0.6389465 at 70iterations 7.6672211E-03 0.2456207 at 80iterations 3.3747251E-03 0.1052399 at 90iterations 1.5967985E-03 5.0689697E-02 at 100iterations 8.5353770E-04 3.1707764E-02 at 110iterations 5.1760144E-04 1.6090393E-02 at 120iterations finished qdiffx linear iterations at : 13:59:45 total time elapsed so far: 11.79000 # loops : 120 mean,max change (kT/e) : 5.1760144E-04 1.6090393E-02 energy calculations done at 11.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.96000 DelPhi exited at 13:59:46 11.964u 0.487s 0:13.16 94.5% 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 13:59:47 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 = 4697 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.305235 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): -57.19100 7.239000 ymin,ymax (A): -49.96800 7.196000 zmin,zma (A): -73.85300 -4.359000 x,y,z range (A): 64.43000 57.16400 69.49400 scale (grids/A): 2.305235 object centre (A): -24.97600 -21.38600 -39.10600 number of atom coordinates read : 4697 total number of charged atoms : 4543 net assigned charge : 10.00005 assigned positive charge : 709.5159 centred at (gu) : 91.41154 91.09634 84.65881 assigned negative charge : -699.5207 centred at (gu) : 91.09195 91.53389 85.01583 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 206417 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38580 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 91931 mr = 151844 m= 22191 mr = 72828 m= 2925 mr = 16195 m= 165 mr = 1842 m= 1 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 2130 time to turn everything in is 1.760000 number of dielectric boundary points 80848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 36245 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) : 1.536823 object centre at (A) : -24.97600 -21.38600 -39.10600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6014074 -0.2414634 midg,1,midg; midg,igrid,midg 0.1974105 -3.1305939E-02 1,midg,midg; igrid,midg,midg 5.0439271E-03 0.5198749 gauss-seidel spectral radius is 0.9991565 estimated iterations to convergence 272 setup time was (sec) 2.180000 now iterating at: 13:59:49 rms-change max change #iterations 10.10684 281.1175 at 10iterations 5.773851 137.2456 at 20iterations 3.284324 76.06400 at 30iterations 1.854378 37.71460 at 40iterations 1.041785 21.23024 at 50iterations 0.5841002 11.27966 at 60iterations 0.3264606 6.497803 at 70iterations 0.1823803 3.536583 at 80iterations 0.1016872 1.931761 at 90iterations 5.6755438E-02 1.099472 at 100iterations 3.1570427E-02 0.6170292 at 110iterations 1.7566262E-02 0.4119029 at 120iterations 9.7964089E-03 0.1885834 at 130iterations 5.4759607E-03 0.1191940 at 140iterations 3.0721764E-03 5.5526733E-02 at 150iterations 1.7364488E-03 3.1957626E-02 at 160iterations 9.9586009E-04 1.9145012E-02 at 170iterations 5.8508373E-04 1.0841370E-02 at 180iterations finished qdiffx linear iterations at : 14:00:13 total time elapsed so far: 25.14000 # loops : 180 mean,max change (kT/e) : 5.8508373E-04 1.0841370E-02 energy calculations done at 25.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 25.31000 DelPhi exited at 14:00:14 25.315u 0.614s 0:27.09 95.6% 0+0k 0+0io 0pf+0w