Wed Dec 28 11:01:27 PST 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 Wed Dec 28 2011 at 11:01:27 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6410372 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): -3.919000 35.29600 ymin,ymax (A): -4.302000 48.73500 zmin,zma (A): -24.13700 31.39800 x,y,z range (A): 39.21500 53.03700 55.53500 scale (grids/A): 0.6410372 object centre (A): 15.68850 22.21650 3.630500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 287.8261 centred at (gu) : 90.11593 92.82070 90.00753 assigned negative charge : -283.8263 centred at (gu) : 90.17662 92.92558 89.94158 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5581 nv = 96 ne = 84 npr = 40147 no. pairs analyzed = 40147 no. exposed pairs = 2393 no. arc points = 16979 no. surface atoms = 818 nbur = 1144 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 274 mr = 3161 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.2500000 number of dielectric boundary points 2663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1692 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 6493 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7915610E-10 1.1960081E-08 midg,1,midg; midg,igrid,midg 8.4489962E-09 -5.9312626E-09 1,midg,midg; igrid,midg,midg 1.1211998E-08 9.5818609E-10 gauss-seidel spectral radius is 0.9873359 estimated iterations to convergence 73 setup time was (sec) 0.5100000 now iterating at: 11:01:28 rms-change max change #iterations 0.1218503 18.43215 at 10iterations 1.2112402E-02 1.763321 at 20iterations 1.2208761E-03 0.2173100 at 30iterations 1.2041831E-04 2.0212173E-02 at 40iterations 1.1975467E-05 1.8253326E-03 at 50iterations finished qdiffx linear iterations at : 11:01:32 total time elapsed so far: 4.600000 # loops : 50 mean,max change (kT/e) : 1.1975467E-05 1.8253326E-03 energy calculations done at 4.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.770000 DelPhi exited at 11:01:32 4.779u 0.381s 0:05.69 90.5% 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 Wed Dec 28 2011 at 11:01:32 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.923112 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): -3.919000 35.29600 ymin,ymax (A): -4.302000 48.73500 zmin,zma (A): -24.13700 31.39800 x,y,z range (A): 39.21500 53.03700 55.53500 scale (grids/A): 1.923112 object centre (A): 15.68850 22.21650 3.630500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 287.8261 centred at (gu) : 90.34788 98.46178 90.02258 assigned negative charge : -283.8263 centred at (gu) : 90.52996 98.77706 89.82490 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 59865 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16979 grid for indexing accessible points = 1.400000 m= 22642 mr = 41844 m= 3363 mr = 17484 m= 156 mr = 2188 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 2342 time to turn everything in is 0.5200000 number of dielectric boundary points 24466 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 14431 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) : 0.6410372 object centre at (A) : 15.68850 22.21650 3.630500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7195081E-02 2.3554895E-02 midg,1,midg; midg,igrid,midg 3.4585897E-02 6.8605720E-04 1,midg,midg; igrid,midg,midg 3.6934011E-03 -1.3591845E-03 gauss-seidel spectral radius is 0.9985815 estimated iterations to convergence 210 setup time was (sec) 0.8200000 now iterating at: 11:01:34 rms-change max change #iterations 3.593548 171.1531 at 10iterations 1.660509 64.68829 at 20iterations 0.7671090 27.10081 at 30iterations 0.3543880 12.29401 at 40iterations 0.1630441 5.877291 at 50iterations 7.5315870E-02 2.471382 at 60iterations 3.4805123E-02 1.164829 at 70iterations 1.6074397E-02 0.5917187 at 80iterations 7.3879603E-03 0.3035669 at 90iterations 3.4234740E-03 0.1140070 at 100iterations 1.5784627E-03 5.3253174E-02 at 110iterations 7.2791404E-04 2.5957108E-02 at 120iterations finished qdiffx linear iterations at : 11:01:44 total time elapsed so far: 11.44000 # loops : 120 mean,max change (kT/e) : 7.2791404E-04 2.5957108E-02 energy calculations done at 11.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.60000 DelPhi exited at 11:01:45 11.609u 0.418s 0:12.69 94.6% 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 Wed Dec 28 2011 at 11:01:45 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.884668 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): -3.919000 35.29600 ymin,ymax (A): -4.302000 48.73500 zmin,zma (A): -24.13700 31.39800 x,y,z range (A): 39.21500 53.03700 55.53500 scale (grids/A): 2.884668 object centre (A): 15.68850 22.21650 3.630500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 287.8261 centred at (gu) : 90.52185 102.6927 90.03395 assigned negative charge : -283.8263 centred at (gu) : 90.79499 103.1656 89.73741 start vw surface at 0.1000000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 138206 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16979 grid for indexing accessible points = 1.400000 m= 72548 mr = 100936 m= 27124 mr = 60763 m= 6150 mr = 22748 m= 722 mr = 4680 m= 45 mr = 445 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 7888 time to turn everything in is 1.280000 number of dielectric boundary points 55204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 14640 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) : 1.923112 object centre at (A) : 15.68850 22.21650 3.630500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.114040 8.7768540E-02 midg,1,midg; midg,igrid,midg 0.3415196 -5.1694565E-02 1,midg,midg; igrid,midg,midg 1.9216878E-02 -6.3605425E-03 gauss-seidel spectral radius is 0.9992319 estimated iterations to convergence 285 setup time was (sec) 1.610000 now iterating at: 11:01:47 rms-change max change #iterations 8.474949 580.0781 at 10iterations 4.859637 114.1473 at 20iterations 2.766552 59.32466 at 30iterations 1.570154 35.41891 at 40iterations 0.8956519 18.80737 at 50iterations 0.5080467 11.08503 at 60iterations 0.2886442 6.334659 at 70iterations 0.1637766 3.436440 at 80iterations 9.3077563E-02 1.931786 at 90iterations 5.2775152E-02 1.071881 at 100iterations 2.9937312E-02 0.6323166 at 110iterations 1.6963134E-02 0.3620415 at 120iterations 9.6399831E-03 0.1877136 at 130iterations 5.4658055E-03 0.1085672 at 140iterations 3.0994981E-03 6.4481258E-02 at 150iterations 1.7602763E-03 3.7956238E-02 at 160iterations 9.9995884E-04 2.1451473E-02 at 170iterations 5.6822458E-04 1.1077404E-02 at 180iterations finished qdiffx linear iterations at : 11:02:05 total time elapsed so far: 18.88000 # loops : 180 mean,max change (kT/e) : 5.6822458E-04 1.1077404E-02 energy calculations done at 18.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.05000 DelPhi exited at 11:02:06 19.051u 0.459s 0:20.47 95.2% 0+0k 0+0io 0pf+0w