Sat Oct 8 11:47:26 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 Sat Oct 8 2011 at 11:47:26 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 = 5559 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 0.5316607 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): 16.00200 78.62700 ymin,ymax (A): 10.96900 76.42600 zmin,zma (A): 8.542000 75.50200 x,y,z range (A): 62.62500 65.45700 66.96000 scale (grids/A): 0.5316607 object centre (A): 47.31450 43.69750 42.02200 number of atom coordinates read : 5559 total number of charged atoms : 5387 net assigned charge : 1.500031 assigned positive charge : 846.9209 centred at (gu) : 89.69264 90.60468 90.45224 assigned negative charge : -845.4273 centred at (gu) : 89.71356 90.60732 90.48430 start vw surface at 0.2800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 9658 nv = 96 ne = 84 npr = 115871 no. pairs analyzed = 115871 no. exposed pairs = 6494 no. arc points = 43960 no. surface atoms = 2174 nbur = 3385 mkacc time = 0.3300000 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= 363 mr = 5341 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.6800000 number of dielectric boundary points 4671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4422 ## 596 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 13125 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5484123E-10 -2.0445207E-10 midg,1,midg; midg,igrid,midg 6.2304870E-11 3.9239254E-11 1,midg,midg; igrid,midg,midg 2.2209475E-10 -9.2035553E-11 gauss-seidel spectral radius is 0.9819444 estimated iterations to convergence 61 setup time was (sec) 0.9600000 now iterating at: 11:47:27 rms-change max change #iterations 9.0512827E-02 13.59044 at 10iterations 7.3249894E-03 1.358253 at 20iterations 1.2244800E-03 0.3046188 at 30iterations 3.1838275E-04 7.4066162E-02 at 40iterations 9.9383476E-05 1.8379211E-02 at 50iterations finished qdiffx linear iterations at : 11:47:30 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 9.9383476E-05 1.8379211E-02 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 11:47:30 4.321u 0.154s 0:04.76 93.9% 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 Sat Oct 8 2011 at 11:47:31 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 = 5559 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 1.594982 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): 16.00200 78.62700 ymin,ymax (A): 10.96900 76.42600 zmin,zma (A): 8.542000 75.50200 x,y,z range (A): 62.62500 65.45700 66.96000 scale (grids/A): 1.594982 object centre (A): 47.31450 43.69750 42.02200 number of atom coordinates read : 5559 total number of charged atoms : 5387 net assigned charge : 1.500031 assigned positive charge : 846.9209 centred at (gu) : 89.07598 91.81250 91.35484 assigned negative charge : -845.4273 centred at (gu) : 89.14034 91.82170 91.45267 start vw surface at 0.2800000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 109426 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43960 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 33452 mr = 78035 m= 3231 mr = 23222 m= 93 mr = 1567 m= 2 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 1792 time to turn everything in is 0.9500000 number of dielectric boundary points 43377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 591 ## 5 charges are in solution ## iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 41004 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) : 0.5316607 object centre at (A) : 47.31450 43.69750 42.02200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4556769E-02 1.6083339E-02 midg,1,midg; midg,igrid,midg 1.4304734E-02 -6.3251606E-03 1,midg,midg; igrid,midg,midg 1.2379750E-03 -6.2374929E-03 gauss-seidel spectral radius is 0.9983295 estimated iterations to convergence 194 setup time was (sec) 1.310000 now iterating at: 11:47:32 rms-change max change #iterations 4.575325 217.3163 at 10iterations 1.974386 63.65418 at 20iterations 0.8529693 26.76877 at 30iterations 0.3697371 10.30774 at 40iterations 0.1602893 5.391487 at 50iterations 6.9554657E-02 1.954774 at 60iterations 3.0244676E-02 0.9046898 at 70iterations 1.3234133E-02 0.3587742 at 80iterations 5.8384999E-03 0.1643906 at 90iterations 2.6004771E-03 7.3963165E-02 at 100iterations 1.1895066E-03 3.8627625E-02 at 110iterations 5.7134917E-04 2.0172119E-02 at 120iterations finished qdiffx linear iterations at : 11:47:40 total time elapsed so far: 9.200000 # loops : 120 mean,max change (kT/e) : 5.7134917E-04 2.0172119E-02 energy calculations done at 9.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.430000 DelPhi exited at 11:47:40 9.438u 0.181s 0:09.92 96.8% 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 Sat Oct 8 2011 at 11:47:40 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 = 5559 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.392473 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): 16.00200 78.62700 ymin,ymax (A): 10.96900 76.42600 zmin,zma (A): 8.542000 75.50200 x,y,z range (A): 62.62500 65.45700 66.96000 scale (grids/A): 2.392473 object centre (A): 47.31450 43.69750 42.02200 number of atom coordinates read : 5559 total number of charged atoms : 5387 net assigned charge : 1.500031 assigned positive charge : 846.9209 centred at (gu) : 88.61335 92.71842 92.03184 assigned negative charge : -845.4273 centred at (gu) : 88.71027 92.73242 92.17908 start vw surface at 0.2600000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 255698 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43960 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 117110 mr = 191324 m= 32577 mr = 93469 m= 5029 mr = 24464 m= 310 mr = 3277 m= 4 mr = 137 m= 0 mr = 0 time to grow re-entrant surface = 1.410000 no. cavity mid-points inaccessible to solvent = 6320 time to turn everything in is 2.340000 number of dielectric boundary points 98057 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 2.520000 number of grid points assigned charge 43020 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) : 1.594982 object centre at (A) : 47.31450 43.69750 42.02200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4227678 0.2198925 midg,1,midg; midg,igrid,midg 0.1949138 -0.1750120 1,midg,midg; igrid,midg,midg 8.1823096E-02 -0.1249853 gauss-seidel spectral radius is 0.9992346 estimated iterations to convergence 285 setup time was (sec) 2.720000 now iterating at: 11:47:43 rms-change max change #iterations 11.99429 301.1115 at 10iterations 7.068548 169.5012 at 20iterations 4.142767 85.60200 at 30iterations 2.421046 55.61662 at 40iterations 1.404830 29.21563 at 50iterations 0.8154600 16.86988 at 60iterations 0.4704245 8.768311 at 70iterations 0.2716759 6.269228 at 80iterations 0.1568663 2.983656 at 90iterations 9.0296999E-02 1.601095 at 100iterations 5.1857077E-02 0.9893341 at 110iterations 2.9827038E-02 0.5814590 at 120iterations 1.7141333E-02 0.3305206 at 130iterations 9.8697376E-03 0.1758347 at 140iterations 5.6746956E-03 0.1066132 at 150iterations 3.2823605E-03 5.9406757E-02 at 160iterations 1.9091205E-03 3.3729553E-02 at 170iterations 1.1166179E-03 2.0610332E-02 at 180iterations finished qdiffx linear iterations at : 11:47:56 total time elapsed so far: 15.42000 # loops : 180 mean,max change (kT/e) : 1.1166179E-03 2.0610332E-02 energy calculations done at 15.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.66000 DelPhi exited at 11:47:57 15.661u 0.204s 0:16.25 97.6% 0+0k 0+0io 0pf+0w