Sun Oct 9 09:05:59 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 09:05:59 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 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: 0.5231217 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): -14.04400 54.00900 ymin,ymax (A): -27.49900 34.97300 zmin,zma (A): 31.34100 81.40300 x,y,z range (A): 68.05300 62.47200 50.06200 scale (grids/A): 0.5231217 object centre (A): 19.98250 3.737001 56.37200 number of atom coordinates read : 2559 total number of charged atoms : 2415 net assigned charge : 7.500017 assigned positive charge : 379.2389 centred at (gu) : 93.62035 91.56143 90.73406 assigned negative charge : -371.7396 centred at (gu) : 93.57430 91.60659 90.72796 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4687 nv = 96 ne = 84 npr = 49346 no. pairs analyzed = 49346 no. exposed pairs = 3649 no. arc points = 26367 no. surface atoms = 1202 nbur = 1357 mkacc time = 0.1100000 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 = 1.624000 m= 168 mr = 2139 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 2716 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2557 ## 387 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6087 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3646506E-10 2.2957888E-10 midg,1,midg; midg,igrid,midg 1.8717815E-10 1.0993686E-10 1,midg,midg; igrid,midg,midg 3.2308371E-11 7.1513273E-10 gauss-seidel spectral radius is 0.9811583 estimated iterations to convergence 60 setup time was (sec) 0.4900000 now iterating at: 09:06:00 rms-change max change #iterations 5.4423984E-02 11.20502 at 10iterations 3.1488587E-03 0.6278782 at 20iterations 2.4613293E-04 5.8305740E-02 at 30iterations 5.0155526E-05 1.5666962E-02 at 40iterations 1.4500385E-05 4.5862198E-03 at 50iterations finished qdiffx linear iterations at : 09:06:02 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 1.4500385E-05 4.5862198E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 09:06:03 3.137u 0.195s 0:03.61 91.9% 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 09:06:03 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.569365 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): -14.04400 54.00900 ymin,ymax (A): -27.49900 34.97300 zmin,zma (A): 31.34100 81.40300 x,y,z range (A): 68.05300 62.47200 50.06200 scale (grids/A): 1.569365 object centre (A): 19.98250 3.737001 56.37200 number of atom coordinates read : 2559 total number of charged atoms : 2415 net assigned charge : 7.500017 assigned positive charge : 379.2389 centred at (gu) : 100.8603 94.68382 92.20158 assigned negative charge : -371.7396 centred at (gu) : 100.7228 94.81951 92.18387 start vw surface at 0.1400000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 51521 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26367 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 14965 mr = 32435 m= 1414 mr = 9658 m= 35 mr = 523 m= 0 mr = 2 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 25317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 355 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 18271 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) : 0.5231217 object centre at (A) : 19.98250 3.737001 56.37200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5618754E-03 6.9118799E-03 midg,1,midg; midg,igrid,midg 8.9598577E-03 2.6072029E-03 1,midg,midg; igrid,midg,midg -8.3269998E-03 -2.4269070E-03 gauss-seidel spectral radius is 0.9979818 estimated iterations to convergence 177 setup time was (sec) 0.6700000 now iterating at: 09:06:03 rms-change max change #iterations 2.731069 136.2846 at 10iterations 1.076191 50.42530 at 20iterations 0.4253137 17.56540 at 30iterations 0.1682180 8.716682 at 40iterations 6.6887975E-02 2.695435 at 50iterations 2.6504487E-02 1.114605 at 60iterations 1.0545937E-02 0.4131136 at 70iterations 4.2094849E-03 0.1766510 at 80iterations 1.6884432E-03 7.3642254E-02 at 90iterations 6.9763011E-04 3.2386780E-02 at 100iterations 3.0133052E-04 1.5592575E-02 at 110iterations 1.4260289E-04 8.4590912E-03 at 120iterations finished qdiffx linear iterations at : 09:06:10 total time elapsed so far: 7.160000 # loops : 120 mean,max change (kT/e) : 1.4260289E-04 8.4590912E-03 energy calculations done at 7.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.350000 DelPhi exited at 09:06:11 7.348u 0.220s 0:07.91 95.5% 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 Sun Oct 9 2011 at 09:06:11 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 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: 2.354048 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): -14.04400 54.00900 ymin,ymax (A): -27.49900 34.97300 zmin,zma (A): 31.34100 81.40300 x,y,z range (A): 68.05300 62.47200 50.06200 scale (grids/A): 2.354048 object centre (A): 19.98250 3.737001 56.37200 number of atom coordinates read : 2559 total number of charged atoms : 2415 net assigned charge : 7.500017 assigned positive charge : 379.2389 centred at (gu) : 106.2904 97.02554 93.30230 assigned negative charge : -371.7396 centred at (gu) : 106.0841 97.22922 93.27560 start vw surface at 0.1500000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 119645 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26367 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 52166 mr = 80347 m= 13998 mr = 39405 m= 1870 mr = 9895 m= 104 mr = 1027 m= 0 mr = 34 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9100000 number of dielectric boundary points 57075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 19281 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) : 1.569365 object centre at (A) : 19.98250 3.737001 56.37200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2671975E-02 0.1139696 midg,1,midg; midg,igrid,midg 0.2869619 3.0397832E-02 1,midg,midg; igrid,midg,midg -0.1862627 -7.5086035E-02 gauss-seidel spectral radius is 0.9990520 estimated iterations to convergence 257 setup time was (sec) 1.200000 now iterating at: 09:06:12 rms-change max change #iterations 7.344574 363.4343 at 10iterations 4.029017 115.3815 at 20iterations 2.189558 62.86581 at 30iterations 1.181760 32.05952 at 40iterations 0.6370189 18.66646 at 50iterations 0.3415505 8.286582 at 60iterations 0.1831163 4.574335 at 70iterations 9.7891673E-02 2.394635 at 80iterations 5.2518304E-02 1.389801 at 90iterations 2.7974300E-02 0.6540256 at 100iterations 1.4973179E-02 0.3496084 at 110iterations 7.9993615E-03 0.1832409 at 120iterations 4.2736684E-03 0.1000057 at 130iterations 2.2785664E-03 5.5054665E-02 at 140iterations 1.2198797E-03 2.9422760E-02 at 150iterations 6.5306347E-04 1.5159607E-02 at 160iterations 3.5256011E-04 9.4280243E-03 at 170iterations 1.9264377E-04 4.6939850E-03 at 180iterations finished qdiffx linear iterations at : 09:06:22 total time elapsed so far: 11.60000 # loops : 180 mean,max change (kT/e) : 1.9264377E-04 4.6939850E-03 energy calculations done at 11.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.78000 DelPhi exited at 09:06:23 11.785u 0.212s 0:12.27 97.7% 0+0k 0+0io 0pf+0w