Mon Oct 10 17:15:07 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 Mon Oct 10 2011 at 17:15:07 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 = 2848 !!! WARNING: GLU 858 has a net charge of -2.0000 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: 0.5831668 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): -15.01800 46.02800 ymin,ymax (A): -31.51300 27.02800 zmin,zma (A): -7.984000 44.02500 x,y,z range (A): 61.04600 58.54100 52.00900 scale (grids/A): 0.5831668 object centre (A): 15.50500 -2.242500 18.02050 number of atom coordinates read : 2848 total number of charged atoms : 2704 net assigned charge : -1.499988 assigned positive charge : 426.8203 centred at (gu) : 87.90036 90.22985 90.34441 assigned negative charge : -428.3214 centred at (gu) : 88.03217 90.20903 90.35509 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6243 nv = 96 ne = 84 npr = 59157 no. pairs analyzed = 59157 no. exposed pairs = 3494 no. arc points = 24527 no. surface atoms = 1175 nbur = 1673 mkacc time = 0.1600000 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 = 1.484000 m= 313 mr = 3322 m= 0 mr = 14 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3400000 number of dielectric boundary points 3220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2495 ## 285 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8033 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7157302E-10 -7.4277001E-10 midg,1,midg; midg,igrid,midg -8.7624413E-10 5.5966051E-11 1,midg,midg; igrid,midg,midg 4.3324189E-09 -2.1900641E-09 gauss-seidel spectral radius is 0.9848087 estimated iterations to convergence 67 setup time was (sec) 0.6300000 now iterating at: 17:15:08 rms-change max change #iterations 9.8276094E-02 16.53947 at 10iterations 7.8054429E-03 1.239244 at 20iterations 6.1424670E-04 9.4560623E-02 at 30iterations 5.2488736E-05 8.3923340E-03 at 40iterations 4.9797991E-06 7.3146820E-04 at 50iterations finished qdiffx linear iterations at : 17:15:12 total time elapsed so far: 4.890000 # loops : 50 mean,max change (kT/e) : 4.9797991E-06 7.3146820E-04 energy calculations done at 4.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.070000 DelPhi exited at 17:15:13 5.074u 0.463s 0:05.91 93.5% 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 Mon Oct 10 2011 at 17:15:13 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 = 2848 !!! WARNING: GLU 858 has a net charge of -2.0000 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: 1.749500 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): -15.01800 46.02800 ymin,ymax (A): -31.51300 27.02800 zmin,zma (A): -7.984000 44.02500 x,y,z range (A): 61.04600 58.54100 52.00900 scale (grids/A): 1.749500 object centre (A): 15.50500 -2.242500 18.02050 number of atom coordinates read : 2848 total number of charged atoms : 2704 net assigned charge : -1.499988 assigned positive charge : 426.8203 centred at (gu) : 83.70054 90.68877 91.03265 assigned negative charge : -428.3214 centred at (gu) : 84.09605 90.62681 91.06516 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68951 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24527 grid for indexing accessible points = 1.400000 m= 21782 mr = 47093 m= 2683 mr = 15282 m= 100 mr = 1507 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 235 time to turn everything in is 0.5800000 number of dielectric boundary points 29605 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 218 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 20967 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) : 0.5831668 object centre at (A) : 15.50500 -2.242500 18.02050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3725717E-03 -2.5875666E-04 midg,1,midg; midg,igrid,midg 1.4942014E-02 8.5010724E-03 1,midg,midg; igrid,midg,midg 2.6092965E-02 -1.4992756E-02 gauss-seidel spectral radius is 0.9984094 estimated iterations to convergence 199 setup time was (sec) 0.9100000 now iterating at: 17:15:14 rms-change max change #iterations 3.789369 168.4414 at 10iterations 1.668594 65.95196 at 20iterations 0.7373113 24.98742 at 30iterations 0.3242694 10.64365 at 40iterations 0.1427377 4.913548 at 50iterations 6.3493103E-02 2.259047 at 60iterations 2.7896255E-02 0.8980408 at 70iterations 1.2347784E-02 0.4081616 at 80iterations 5.4491805E-03 0.1820087 at 90iterations 2.3959531E-03 8.1992865E-02 at 100iterations 1.0586320E-03 3.5307407E-02 at 110iterations 4.6663263E-04 1.5552521E-02 at 120iterations finished qdiffx linear iterations at : 17:15:25 total time elapsed so far: 11.55000 # loops : 120 mean,max change (kT/e) : 4.6663263E-04 1.5552521E-02 energy calculations done at 11.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.72000 DelPhi exited at 17:15:26 11.725u 0.508s 0:12.59 97.0% 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 Mon Oct 10 2011 at 17:15:26 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 = 2848 !!! WARNING: GLU 858 has a net charge of -2.0000 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: 2.624251 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): -15.01800 46.02800 ymin,ymax (A): -31.51300 27.02800 zmin,zma (A): -7.984000 44.02500 x,y,z range (A): 61.04600 58.54100 52.00900 scale (grids/A): 2.624251 object centre (A): 15.50500 -2.242500 18.02050 number of atom coordinates read : 2848 total number of charged atoms : 2704 net assigned charge : -1.499988 assigned positive charge : 426.8203 centred at (gu) : 80.55063 91.03296 91.54882 assigned negative charge : -428.3214 centred at (gu) : 81.14399 90.94000 91.59783 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 159957 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24527 grid for indexing accessible points = 1.400000 m= 73621 mr = 115094 m= 23374 mr = 58495 m= 4475 mr = 18099 m= 466 mr = 3145 m= 17 mr = 295 m= 0 mr = 5 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 760 time to turn everything in is 1.500000 number of dielectric boundary points 66777 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 21626 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) : 1.749500 object centre at (A) : 15.50500 -2.242500 18.02050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9365651E-02 4.3006871E-02 midg,1,midg; midg,igrid,midg 0.1742821 0.1547589 1,midg,midg; igrid,midg,midg 0.6755684 -0.2213940 gauss-seidel spectral radius is 0.9992040 estimated iterations to convergence 280 setup time was (sec) 1.880000 now iterating at: 17:15:28 rms-change max change #iterations 9.332759 313.8271 at 10iterations 5.347214 135.5612 at 20iterations 3.050448 69.69102 at 30iterations 1.732110 35.78569 at 40iterations 0.9831441 22.46286 at 50iterations 0.5546647 11.03365 at 60iterations 0.3142776 6.658699 at 70iterations 0.1771301 3.485929 at 80iterations 9.9871509E-02 2.177155 at 90iterations 5.6255564E-02 1.220367 at 100iterations 3.1731278E-02 0.6268873 at 110iterations 1.7868808E-02 0.3469324 at 120iterations 1.0061852E-02 0.1991901 at 130iterations 5.6487932E-03 0.1102870 at 140iterations 3.1906818E-03 6.2450647E-02 at 150iterations 1.7930577E-03 3.8010359E-02 at 160iterations 1.0087405E-03 1.9464493E-02 at 170iterations 5.6957960E-04 1.0781765E-02 at 180iterations finished qdiffx linear iterations at : 17:15:46 total time elapsed so far: 19.59000 # loops : 180 mean,max change (kT/e) : 5.6957960E-04 1.0781765E-02 energy calculations done at 19.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.75000 DelPhi exited at 17:15:46 19.753u 0.543s 0:20.61 98.4% 0+0k 0+0io 0pf+0w