Sat Oct 8 15:52:05 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 15:52:05 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 = 2338 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: 0.6566448 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): -2.139000 46.45300 ymin,ymax (A): -16.96200 29.55400 zmin,zma (A): -17.97200 36.24300 x,y,z range (A): 48.59200 46.51600 54.21500 scale (grids/A): 0.6566448 object centre (A): 22.15700 6.296000 9.135500 number of atom coordinates read : 2338 total number of charged atoms : 2252 net assigned charge : 2.000001 assigned positive charge : 346.4181 centred at (gu) : 90.20518 88.83884 90.11269 assigned negative charge : -344.4187 centred at (gu) : 90.19233 88.94630 90.20535 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6777 nv = 96 ne = 84 npr = 47449 no. pairs analyzed = 47449 no. exposed pairs = 2880 no. arc points = 19971 no. surface atoms = 985 nbur = 1353 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 398 mr = 3789 m= 4 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.2700000 number of dielectric boundary points 3328 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2003 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8146 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8757776E-08 -1.0884866E-08 midg,1,midg; midg,igrid,midg 2.7561409E-08 -1.0155419E-08 1,midg,midg; igrid,midg,midg 2.2801676E-09 6.7860286E-09 gauss-seidel spectral radius is 0.9879580 estimated iterations to convergence 74 setup time was (sec) 0.5200000 now iterating at: 15:52:06 rms-change max change #iterations 0.1534913 26.32495 at 10iterations 1.5914645E-02 2.075287 at 20iterations 1.7266190E-03 0.2399960 at 30iterations 2.0413558E-04 2.8435707E-02 at 40iterations 3.1658667E-05 5.1202774E-03 at 50iterations finished qdiffx linear iterations at : 15:52:08 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 3.1658667E-05 5.1202774E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 15:52:09 3.333u 0.209s 0:03.85 91.6% 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 Sat Oct 8 2011 at 15:52:09 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 = 2338 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.969934 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): -2.139000 46.45300 ymin,ymax (A): -16.96200 29.55400 zmin,zma (A): -17.97200 36.24300 x,y,z range (A): 48.59200 46.51600 54.21500 scale (grids/A): 1.969934 object centre (A): 22.15700 6.296000 9.135500 number of atom coordinates read : 2338 total number of charged atoms : 2252 net assigned charge : 2.000001 assigned positive charge : 346.4181 centred at (gu) : 90.61512 86.51587 90.33772 assigned negative charge : -344.4187 centred at (gu) : 90.57703 86.83884 90.61607 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73281 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19971 grid for indexing accessible points = 1.400000 m= 26812 mr = 51386 m= 4834 mr = 20066 m= 341 mr = 3219 m= 7 mr = 146 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 762 time to turn everything in is 0.5200000 number of dielectric boundary points 30458 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 17780 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) : 0.6566448 object centre at (A) : 22.15700 6.296000 9.135500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1515460E-02 -2.2702858E-02 midg,1,midg; midg,igrid,midg 2.4759522E-02 -7.8709181E-03 1,midg,midg; igrid,midg,midg -3.6501903E-03 -4.2665765E-02 gauss-seidel spectral radius is 0.9986947 estimated iterations to convergence 219 setup time was (sec) 0.8200000 now iterating at: 15:52:10 rms-change max change #iterations 4.249544 196.2410 at 10iterations 2.011925 84.54816 at 20iterations 0.9556992 31.83620 at 30iterations 0.4567863 13.70543 at 40iterations 0.2170974 7.010255 at 50iterations 0.1037112 3.083076 at 60iterations 4.9301557E-02 1.528273 at 70iterations 2.3495603E-02 0.7637324 at 80iterations 1.1185626E-02 0.3549604 at 90iterations 5.3279973E-03 0.1587830 at 100iterations 2.5606994E-03 7.4543953E-02 at 110iterations 1.2166059E-03 3.8821697E-02 at 120iterations finished qdiffx linear iterations at : 15:52:17 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 1.2166059E-03 3.8821697E-02 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 15:52:17 7.542u 0.236s 0:08.07 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 Sat Oct 8 2011 at 15:52:17 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 = 2338 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: 2.954902 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): -2.139000 46.45300 ymin,ymax (A): -16.96200 29.55400 zmin,zma (A): -17.97200 36.24300 x,y,z range (A): 48.59200 46.51600 54.21500 scale (grids/A): 2.954902 object centre (A): 22.15700 6.296000 9.135500 number of atom coordinates read : 2338 total number of charged atoms : 2252 net assigned charge : 2.000001 assigned positive charge : 346.4181 centred at (gu) : 90.92259 84.77375 90.50647 assigned negative charge : -344.4187 centred at (gu) : 90.86556 85.25826 90.92406 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 169738 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19971 grid for indexing accessible points = 1.400000 m= 85573 mr = 124440 m= 32712 mr = 70493 m= 9087 mr = 26828 m= 1489 mr = 7119 m= 119 mr = 1061 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 2651 time to turn everything in is 1.350000 number of dielectric boundary points 68719 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 18016 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) : 1.969934 object centre at (A) : 22.15700 6.296000 9.135500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2764276 -0.2929721 midg,1,midg; midg,igrid,midg 0.2057184 -0.1171551 1,midg,midg; igrid,midg,midg -4.8532199E-02 -0.6459059 gauss-seidel spectral radius is 0.9992700 estimated iterations to convergence 292 setup time was (sec) 1.670000 now iterating at: 15:52:19 rms-change max change #iterations 9.816651 552.0878 at 10iterations 5.752320 129.1180 at 20iterations 3.364924 73.18224 at 30iterations 1.963673 37.47765 at 40iterations 1.140255 21.20928 at 50iterations 0.6616738 13.79334 at 60iterations 0.3840996 7.778430 at 70iterations 0.2225880 4.023664 at 80iterations 0.1288305 2.312862 at 90iterations 7.4609287E-02 1.321974 at 100iterations 4.3109726E-02 0.8374786 at 110iterations 2.4926933E-02 0.4170499 at 120iterations 1.4386113E-02 0.2853546 at 130iterations 8.3023943E-03 0.1686344 at 140iterations 4.8020603E-03 7.7321172E-02 at 150iterations 2.7708099E-03 4.9870014E-02 at 160iterations 1.5971644E-03 2.6779175E-02 at 170iterations 9.2479575E-04 1.6689301E-02 at 180iterations finished qdiffx linear iterations at : 15:52:30 total time elapsed so far: 12.12000 # loops : 180 mean,max change (kT/e) : 9.2479575E-04 1.6689301E-02 energy calculations done at 12.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.30000 DelPhi exited at 15:52:30 12.301u 0.249s 0:12.89 97.2% 0+0k 0+0io 0pf+0w