Sun Oct 9 13:03:54 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 Sun Oct 9 2011 at 13:03:54 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2382 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: 0.6833407 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): -13.86900 34.80700 ymin,ymax (A): -2.221000 49.87600 zmin,zma (A): 41.81300 83.96600 x,y,z range (A): 48.67600 52.09700 42.15300 scale (grids/A): 0.6833407 object centre (A): 10.46900 23.82750 62.88950 number of atom coordinates read : 2382 total number of charged atoms : 2240 net assigned charge : 3.500025 assigned positive charge : 368.2531 centred at (gu) : 89.83332 89.22456 90.85179 assigned negative charge : -364.7535 centred at (gu) : 89.84185 89.05170 90.93807 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7576 nv = 96 ne = 84 npr = 47541 no. pairs analyzed = 47541 no. exposed pairs = 2933 no. arc points = 20616 no. surface atoms = 984 nbur = 1398 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 419 mr = 4218 m= 4 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.1900000 number of dielectric boundary points 3704 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2033 ## 240 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8644 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8350045E-08 -1.4042830E-08 midg,1,midg; midg,igrid,midg -4.8358533E-08 6.2738025E-08 1,midg,midg; igrid,midg,midg 2.0685613E-08 1.3921223E-08 gauss-seidel spectral radius is 0.9888755 estimated iterations to convergence 77 setup time was (sec) 0.3800000 now iterating at: 13:03:55 rms-change max change #iterations 0.1883760 25.10114 at 10iterations 2.1901950E-02 2.928543 at 20iterations 2.7264797E-03 0.3503799 at 30iterations 4.2798716E-04 5.4292679E-02 at 40iterations 1.0058457E-04 1.2286186E-02 at 50iterations finished qdiffx linear iterations at : 13:03:57 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.0058457E-04 1.2286186E-02 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 13:03:58 3.372u 0.170s 0:03.82 92.6% 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 Sun Oct 9 2011 at 13:03:58 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2382 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: 2.050022 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): -13.86900 34.80700 ymin,ymax (A): -2.221000 49.87600 zmin,zma (A): 41.81300 83.96600 x,y,z range (A): 48.67600 52.09700 42.15300 scale (grids/A): 2.050022 object centre (A): 10.46900 23.82750 62.88950 number of atom coordinates read : 2382 total number of charged atoms : 2240 net assigned charge : 3.500025 assigned positive charge : 368.2531 centred at (gu) : 89.49956 87.67323 92.55472 assigned negative charge : -364.7535 centred at (gu) : 89.52553 87.15504 92.81406 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 80164 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20616 grid for indexing accessible points = 1.400000 m= 30574 mr = 56033 m= 5501 mr = 22935 m= 476 mr = 3543 m= 6 mr = 263 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 644 time to turn everything in is 0.3900000 number of dielectric boundary points 33947 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 128 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 17764 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) : 0.6833407 object centre at (A) : 10.46900 23.82750 62.88950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3283378E-02 4.0859561E-03 midg,1,midg; midg,igrid,midg -6.6763490E-02 1.9541167E-02 1,midg,midg; igrid,midg,midg 8.8370871E-03 3.0231956E-02 gauss-seidel spectral radius is 0.9987954 estimated iterations to convergence 228 setup time was (sec) 0.6100000 now iterating at: 13:03:59 rms-change max change #iterations 4.779716 255.9520 at 10iterations 2.320704 85.67204 at 20iterations 1.142750 34.43209 at 30iterations 0.5601454 16.87198 at 40iterations 0.2742220 9.154126 at 50iterations 0.1348272 4.385705 at 60iterations 6.6146232E-02 2.067051 at 70iterations 3.2480720E-02 0.9569964 at 80iterations 1.6022179E-02 0.4613094 at 90iterations 7.9178559E-03 0.2326889 at 100iterations 3.9400877E-03 0.1266191 at 110iterations 1.9986324E-03 6.1269760E-02 at 120iterations finished qdiffx linear iterations at : 13:04:06 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 1.9986324E-03 6.1269760E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 13:04:06 7.799u 0.198s 0:08.29 96.2% 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 Sun Oct 9 2011 at 13:04:06 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2382 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: 3.075033 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): -13.86900 34.80700 ymin,ymax (A): -2.221000 49.87600 zmin,zma (A): 41.81300 83.96600 x,y,z range (A): 48.67600 52.09700 42.15300 scale (grids/A): 3.075033 object centre (A): 10.46900 23.82750 62.88950 number of atom coordinates read : 2382 total number of charged atoms : 2240 net assigned charge : 3.500025 assigned positive charge : 368.2531 centred at (gu) : 89.24921 86.50970 93.83205 assigned negative charge : -364.7535 centred at (gu) : 89.28825 85.73249 94.22094 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 184695 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20616 grid for indexing accessible points = 1.400000 m= 96668 mr = 134925 m= 37517 mr = 79815 m= 10194 mr = 30686 m= 1987 mr = 7711 m= 242 mr = 1540 m= 6 mr = 150 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 2372 time to turn everything in is 1.040000 number of dielectric boundary points 76482 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 17920 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) : 2.050022 object centre at (A) : 10.46900 23.82750 62.88950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5414412 -6.7925155E-02 midg,1,midg; midg,igrid,midg -0.6636906 0.3533442 1,midg,midg; igrid,midg,midg -0.1213496 0.2894481 gauss-seidel spectral radius is 0.9992898 estimated iterations to convergence 296 setup time was (sec) 1.290000 now iterating at: 13:04:08 rms-change max change #iterations 10.79677 466.7842 at 10iterations 6.348720 133.4165 at 20iterations 3.737201 71.18420 at 30iterations 2.195569 49.14828 at 40iterations 1.290599 25.96552 at 50iterations 0.7556612 13.10198 at 60iterations 0.4410833 7.275360 at 70iterations 0.2578710 4.329105 at 80iterations 0.1509490 2.606801 at 90iterations 8.8135146E-02 1.652955 at 100iterations 5.1514283E-02 0.8154403 at 110iterations 3.0049469E-02 0.5003586 at 120iterations 1.7596306E-02 0.3055115 at 130iterations 1.0341551E-02 0.1924915 at 140iterations 6.1171949E-03 0.1060295 at 150iterations 3.6546213E-03 6.4517975E-02 at 160iterations 2.2284079E-03 4.3534279E-02 at 170iterations 1.3968509E-03 2.9481888E-02 at 180iterations finished qdiffx linear iterations at : 13:04:19 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 1.3968509E-03 2.9481888E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 13:04:20 12.891u 0.194s 0:13.36 97.9% 0+0k 0+0io 0pf+0w