Tue Oct 11 03:22:18 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 Tue Oct 11 2011 at 03:22:18 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2469 !!! WARNING: HIR 128 has a net charge of 0.5140 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: 0.5929380 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): -25.85000 24.23000 ymin,ymax (A): -1.692000 54.73800 zmin,zma (A): -35.49400 24.54600 x,y,z range (A): 50.08000 56.43000 60.04000 scale (grids/A): 0.5929380 object centre (A): -0.8100004 26.52300 -5.474002 number of atom coordinates read : 2469 total number of charged atoms : 2323 net assigned charge : 2.514014 assigned positive charge : 368.0710 centred at (gu) : 88.63331 92.28131 92.45415 assigned negative charge : -365.5579 centred at (gu) : 88.57452 92.13259 92.31973 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5839 nv = 96 ne = 84 npr = 48383 no. pairs analyzed = 48383 no. exposed pairs = 3259 no. arc points = 23941 no. surface atoms = 1099 nbur = 1370 mkacc time = 0.1300000 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 = 1.456000 m= 249 mr = 2891 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 48 time to turn everything in is 0.3300000 number of dielectric boundary points 3186 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2369 ## 264 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7204 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7126691E-09 7.5757765E-09 midg,1,midg; midg,igrid,midg -2.0192539E-09 7.9146734E-09 1,midg,midg; igrid,midg,midg -1.3151158E-09 1.6504826E-09 gauss-seidel spectral radius is 0.9852805 estimated iterations to convergence 68 setup time was (sec) 0.6100000 now iterating at: 03:22:18 rms-change max change #iterations 9.8777324E-02 17.86948 at 10iterations 8.0118412E-03 1.432549 at 20iterations 6.7017786E-04 0.1156788 at 30iterations 5.3834236E-05 9.1304779E-03 at 40iterations 4.5155857E-06 6.8473816E-04 at 50iterations finished qdiffx linear iterations at : 03:22:22 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 4.5155857E-06 6.8473816E-04 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 03:22:22 4.116u 0.276s 0:04.71 92.9% 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 Tue Oct 11 2011 at 03:22:22 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2469 !!! WARNING: HIR 128 has a net charge of 0.5140 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: 1.778814 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): -25.85000 24.23000 ymin,ymax (A): -1.692000 54.73800 zmin,zma (A): -35.49400 24.54600 x,y,z range (A): 50.08000 56.43000 60.04000 scale (grids/A): 1.778814 object centre (A): -0.8100004 26.52300 -5.474002 number of atom coordinates read : 2469 total number of charged atoms : 2323 net assigned charge : 2.514014 assigned positive charge : 368.0710 centred at (gu) : 85.89961 96.84364 97.36192 assigned negative charge : -365.5579 centred at (gu) : 85.72351 96.39761 96.95903 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 62982 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23941 grid for indexing accessible points = 1.400000 m= 20159 mr = 40831 m= 2489 mr = 14202 m= 107 mr = 1382 m= 0 mr = 21 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 770 time to turn everything in is 0.5900000 number of dielectric boundary points 29301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 18090 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) : 0.5929380 object centre at (A) : -0.8100004 26.52300 -5.474002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6045639E-03 3.3876728E-02 midg,1,midg; midg,igrid,midg -6.3658762E-03 2.1176359E-02 1,midg,midg; igrid,midg,midg -3.1508959E-04 3.7950866E-03 gauss-seidel spectral radius is 0.9984235 estimated iterations to convergence 200 setup time was (sec) 0.8900000 now iterating at: 03:22:23 rms-change max change #iterations 3.591175 183.8381 at 10iterations 1.579985 83.90641 at 20iterations 0.6972311 25.57259 at 30iterations 0.3074870 10.59729 at 40iterations 0.1352784 4.599918 at 50iterations 5.9786811E-02 2.216450 at 60iterations 2.6496619E-02 0.9653320 at 70iterations 1.1661896E-02 0.4176526 at 80iterations 5.1464364E-03 0.1871567 at 90iterations 2.2773545E-03 7.8628540E-02 at 100iterations 1.0091452E-03 3.4239531E-02 at 110iterations 4.4668574E-04 1.5817642E-02 at 120iterations finished qdiffx linear iterations at : 03:22:32 total time elapsed so far: 9.260000 # loops : 120 mean,max change (kT/e) : 4.4668574E-04 1.5817642E-02 energy calculations done at 9.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.430000 DelPhi exited at 03:22:32 9.437u 0.298s 0:10.00 97.2% 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 Tue Oct 11 2011 at 03:22:32 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2469 !!! WARNING: HIR 128 has a net charge of 0.5140 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: 2.668221 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): -25.85000 24.23000 ymin,ymax (A): -1.692000 54.73800 zmin,zma (A): -35.49400 24.54600 x,y,z range (A): 50.08000 56.43000 60.04000 scale (grids/A): 2.668221 object centre (A): -0.8100004 26.52300 -5.474002 number of atom coordinates read : 2469 total number of charged atoms : 2323 net assigned charge : 2.514014 assigned positive charge : 368.0710 centred at (gu) : 83.84922 100.2653 101.0429 assigned negative charge : -365.5579 centred at (gu) : 83.58523 99.59641 100.4385 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 145985 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23941 grid for indexing accessible points = 1.400000 m= 66918 mr = 99919 m= 21530 mr = 53124 m= 4058 mr = 16713 m= 417 mr = 2814 m= 16 mr = 239 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 2396 time to turn everything in is 1.390000 number of dielectric boundary points 66115 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 18577 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) : 1.778814 object centre at (A) : -0.8100004 26.52300 -5.474002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4414467E-02 0.5624554 midg,1,midg; midg,igrid,midg -4.6372242E-02 0.1911800 1,midg,midg; igrid,midg,midg -2.3879813E-02 4.1822020E-02 gauss-seidel spectral radius is 0.9991970 estimated iterations to convergence 279 setup time was (sec) 1.720000 now iterating at: 03:22:34 rms-change max change #iterations 8.761453 289.3364 at 10iterations 5.009032 133.1144 at 20iterations 2.835063 68.28938 at 30iterations 1.598665 38.89483 at 40iterations 0.9010293 22.19617 at 50iterations 0.5077361 13.22130 at 60iterations 0.2850588 5.977905 at 70iterations 0.1598752 3.418546 at 80iterations 8.9886434E-02 1.926203 at 90iterations 5.0441630E-02 1.098485 at 100iterations 2.8273012E-02 0.5687546 at 110iterations 1.5861433E-02 0.3456688 at 120iterations 8.9032697E-03 0.1853561 at 130iterations 4.9826349E-03 0.1095009 at 140iterations 2.7990760E-03 6.0666561E-02 at 150iterations 1.5756976E-03 3.2859802E-02 at 160iterations 8.8013621E-04 1.6970634E-02 at 170iterations 4.9596076E-04 1.1174679E-02 at 180iterations finished qdiffx linear iterations at : 03:22:48 total time elapsed so far: 15.47000 # loops : 180 mean,max change (kT/e) : 4.9596076E-04 1.1174679E-02 energy calculations done at 15.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.65000 DelPhi exited at 03:22:49 15.652u 0.330s 0:16.32 97.9% 0+0k 0+0io 0pf+0w