Wed Dec 21 14:21:09 PST 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 Wed Dec 21 2011 at 14:21:09 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5521606 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): -35.22200 11.77700 ymin,ymax (A): -2.7999997E-02 42.96300 zmin,zma (A): -3.574000 60.90000 x,y,z range (A): 46.99900 42.99100 64.47400 scale (grids/A): 0.5521606 object centre (A): -11.72250 21.46750 28.66300 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 289.4000 centred at (gu) : 89.96931 89.42870 89.50854 assigned negative charge : -287.4003 centred at (gu) : 89.88479 89.57466 89.51290 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 3981 nv = 96 ne = 84 npr = 40373 no. pairs analyzed = 40373 no. exposed pairs = 2409 no. arc points = 17225 no. surface atoms = 824 nbur = 1146 mkacc time = 0.1200000 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 = 1.568000 m= 134 mr = 2101 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 2006 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1799 ## 263 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 5097 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9976056E-10 1.1624540E-10 midg,1,midg; midg,igrid,midg 1.0696488E-09 -5.6211613E-10 1,midg,midg; igrid,midg,midg -3.0980410E-10 6.0124045E-10 gauss-seidel spectral radius is 0.9830051 estimated iterations to convergence 63 setup time was (sec) 0.5900000 now iterating at: 14:21:10 rms-change max change #iterations 5.9436694E-02 12.66089 at 10iterations 4.0054624E-03 0.7677307 at 20iterations 2.7244855E-04 6.7317963E-02 at 30iterations 1.8603128E-05 4.5623779E-03 at 40iterations 1.3224877E-06 2.7084351E-04 at 50iterations finished qdiffx linear iterations at : 14:21:14 total time elapsed so far: 4.900000 # loops : 50 mean,max change (kT/e) : 1.3224877E-06 2.7084351E-04 energy calculations done at 4.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.080000 DelPhi exited at 14:21:17 5.079u 0.356s 0:07.98 67.9% 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 Wed Dec 21 2011 at 14:21:17 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.656482 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): -35.22200 11.77700 ymin,ymax (A): -2.7999997E-02 42.96300 zmin,zma (A): -3.574000 60.90000 x,y,z range (A): 46.99900 42.99100 64.47400 scale (grids/A): 1.656482 object centre (A): -11.72250 21.46750 28.66300 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 289.4000 centred at (gu) : 89.90804 88.28606 88.52573 assigned negative charge : -287.4003 centred at (gu) : 89.65446 88.72418 88.53893 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 43621 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17225 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 14123 mr = 29542 m= 1534 mr = 10322 m= 46 mr = 824 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 692 time to turn everything in is 0.4200000 number of dielectric boundary points 18635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 241 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 14136 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) : 0.5521606 object centre at (A) : -11.72250 21.46750 28.66300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9521784E-02 1.5072342E-02 midg,1,midg; midg,igrid,midg 1.6393301E-03 -5.8127199E-03 1,midg,midg; igrid,midg,midg -2.7514882E-03 -2.3541013E-04 gauss-seidel spectral radius is 0.9981134 estimated iterations to convergence 183 setup time was (sec) 0.7900000 now iterating at: 14:21:19 rms-change max change #iterations 2.672991 180.3702 at 10iterations 1.094085 51.25661 at 20iterations 0.4499726 19.52261 at 30iterations 0.1838311 7.766896 at 40iterations 7.5641744E-02 2.946121 at 50iterations 3.0930236E-02 1.230690 at 60iterations 1.2654243E-02 0.5521188 at 70iterations 5.1903357E-03 0.2367363 at 80iterations 2.1245922E-03 0.1119385 at 90iterations 8.7641715E-04 4.1809082E-02 at 100iterations 3.5723555E-04 1.6908646E-02 at 110iterations 1.4647085E-04 6.5026283E-03 at 120iterations finished qdiffx linear iterations at : 14:21:30 total time elapsed so far: 11.30000 # loops : 120 mean,max change (kT/e) : 1.4647085E-04 6.5026283E-03 energy calculations done at 11.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.49000 DelPhi exited at 14:21:38 11.488u 0.442s 0:20.37 58.5% 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 Wed Dec 21 2011 at 14:21:38 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.484723 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): -35.22200 11.77700 ymin,ymax (A): -2.7999997E-02 42.96300 zmin,zma (A): -3.574000 60.90000 x,y,z range (A): 46.99900 42.99100 64.47400 scale (grids/A): 2.484723 object centre (A): -11.72250 21.46750 28.66300 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 289.4000 centred at (gu) : 89.86196 87.42912 87.78860 assigned negative charge : -287.4003 centred at (gu) : 89.48168 88.08627 87.80837 start vw surface at 0.1400000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 101107 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17225 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 48002 mr = 71648 m= 14530 mr = 39259 m= 2487 mr = 11504 m= 157 mr = 1738 m= 1 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.5500001 no. cavity mid-points inaccessible to solvent = 2387 time to turn everything in is 0.9900000 number of dielectric boundary points 42062 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 14691 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) : 1.656482 object centre at (A) : -11.72250 21.46750 28.66300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2419816 0.1586675 midg,1,midg; midg,igrid,midg -1.6591996E-03 -9.6906483E-02 1,midg,midg; igrid,midg,midg -4.8214324E-02 -2.6778825E-02 gauss-seidel spectral radius is 0.9990772 estimated iterations to convergence 260 setup time was (sec) 1.280000 now iterating at: 14:21:40 rms-change max change #iterations 6.771360 264.4983 at 10iterations 3.681787 117.3623 at 20iterations 1.990946 62.61146 at 30iterations 1.072620 29.21394 at 40iterations 0.5766074 13.81202 at 50iterations 0.3100534 7.824051 at 60iterations 0.1668306 3.895050 at 70iterations 8.9804709E-02 2.161736 at 80iterations 4.8140023E-02 1.151830 at 90iterations 2.5882078E-02 0.6487637 at 100iterations 1.3900796E-02 0.3503361 at 110iterations 7.4576512E-03 0.2144432 at 120iterations 4.0007369E-03 0.1029663 at 130iterations 2.1472350E-03 5.0451756E-02 at 140iterations 1.1515387E-03 3.0554771E-02 at 150iterations 6.1924086E-04 1.5682220E-02 at 160iterations 3.3236854E-04 8.2778931E-03 at 170iterations 1.7876893E-04 4.3811798E-03 at 180iterations finished qdiffx linear iterations at : 14:21:57 total time elapsed so far: 18.68000 # loops : 180 mean,max change (kT/e) : 1.7876893E-04 4.3811798E-03 energy calculations done at 18.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.88000 DelPhi exited at 14:22:06 18.879u 0.363s 0:28.04 68.5% 0+0k 0+0io 0pf+0w