Mon Oct 10 10:30:45 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 Mon Oct 10 2011 at 10:30:45 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3029 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5433870 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): -22.47700 43.03800 ymin,ymax (A): -10.77200 44.17500 zmin,zma (A): -1.635000 57.92200 x,y,z range (A): 65.51500 54.94700 59.55700 scale (grids/A): 0.5433870 object centre (A): 10.28050 16.70150 28.14350 number of atom coordinates read : 3029 total number of charged atoms : 2887 net assigned charge : 5.000008 assigned positive charge : 448.9315 centred at (gu) : 92.47373 90.81252 86.55575 assigned negative charge : -443.9322 centred at (gu) : 92.58403 90.82804 86.46568 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6151 nv = 96 ne = 84 npr = 56588 no. pairs analyzed = 56588 no. exposed pairs = 4798 no. arc points = 34018 no. surface atoms = 1577 nbur = 1452 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 = 1.568000 m= 271 mr = 2615 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3303 ## 420 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7881 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6223054E-10 3.6114547E-10 midg,1,midg; midg,igrid,midg 3.3229949E-10 2.7105695E-10 1,midg,midg; igrid,midg,midg 5.1844473E-10 -6.5916145E-10 gauss-seidel spectral radius is 0.9825663 estimated iterations to convergence 62 setup time was (sec) 0.5600000 now iterating at: 10:30:46 rms-change max change #iterations 7.1061753E-02 14.91286 at 10iterations 4.5753750E-03 0.8138313 at 20iterations 3.1357893E-04 5.0489426E-02 at 30iterations 2.9031344E-05 4.0454865E-03 at 40iterations 5.0029726E-06 6.0963631E-04 at 50iterations finished qdiffx linear iterations at : 10:30:48 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 5.0029726E-06 6.0963631E-04 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 10:30:49 3.340u 0.229s 0:03.86 92.2% 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 Mon Oct 10 2011 at 10:30:49 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3029 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.630161 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): -22.47700 43.03800 ymin,ymax (A): -10.77200 44.17500 zmin,zma (A): -1.635000 57.92200 x,y,z range (A): 65.51500 54.94700 59.55700 scale (grids/A): 1.630161 object centre (A): 10.28050 16.70150 28.14350 number of atom coordinates read : 3029 total number of charged atoms : 2887 net assigned charge : 5.000008 assigned positive charge : 448.9315 centred at (gu) : 97.42057 92.43688 79.66649 assigned negative charge : -443.9322 centred at (gu) : 97.75192 92.48357 79.39630 start vw surface at 0.1800000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 66751 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34018 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 20292 mr = 40570 m= 2182 mr = 12547 m= 58 mr = 880 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 35285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 336 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 22144 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) : 0.5433870 object centre at (A) : 10.28050 16.70150 28.14350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4605606E-03 1.0085065E-02 midg,1,midg; midg,igrid,midg 9.1443881E-03 1.3582732E-02 1,midg,midg; igrid,midg,midg 8.4531102E-03 -3.5038371E-02 gauss-seidel spectral radius is 0.9981991 estimated iterations to convergence 187 setup time was (sec) 0.8100000 now iterating at: 10:30:50 rms-change max change #iterations 3.316630 153.0942 at 10iterations 1.378917 53.67943 at 20iterations 0.5728915 24.10467 at 30iterations 0.2385942 8.938692 at 40iterations 9.9220149E-02 3.871702 at 50iterations 4.1311670E-02 1.602829 at 60iterations 1.7266713E-02 0.6196713 at 70iterations 7.2212545E-03 0.2763133 at 80iterations 3.0062911E-03 0.1342297 at 90iterations 1.2560566E-03 4.6089172E-02 at 100iterations 5.2492757E-04 1.9699097E-02 at 110iterations 2.2028066E-04 9.0366006E-03 at 120iterations finished qdiffx linear iterations at : 10:30:56 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 2.2028066E-04 9.0366006E-03 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 10:30:57 7.601u 0.210s 0:08.10 96.4% 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 10:30:57 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3029 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.445242 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): -22.47700 43.03800 ymin,ymax (A): -10.77200 44.17500 zmin,zma (A): -1.635000 57.92200 x,y,z range (A): 65.51500 54.94700 59.55700 scale (grids/A): 2.445242 object centre (A): 10.28050 16.70150 28.14350 number of atom coordinates read : 3029 total number of charged atoms : 2887 net assigned charge : 5.000008 assigned positive charge : 448.9315 centred at (gu) : 101.1307 93.65516 74.49951 assigned negative charge : -443.9322 centred at (gu) : 101.6278 93.72533 74.09445 start vw surface at 0.1800000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 154604 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34018 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 68603 mr = 100906 m= 19919 mr = 50556 m= 3340 mr = 13666 m= 217 mr = 1931 m= 6 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.170000 number of dielectric boundary points 79558 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 23065 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) : 1.630161 object centre at (A) : 10.28050 16.70150 28.14350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1308571 0.1111680 midg,1,midg; midg,igrid,midg 0.1380710 0.1896129 1,midg,midg; igrid,midg,midg 0.3716950 -0.7529431 gauss-seidel spectral radius is 0.9991491 estimated iterations to convergence 271 setup time was (sec) 1.480000 now iterating at: 10:30:59 rms-change max change #iterations 8.968586 277.5416 at 10iterations 5.196016 151.0792 at 20iterations 2.967469 93.12727 at 30iterations 1.677519 44.24832 at 40iterations 0.9422167 23.78787 at 50iterations 0.5272180 14.32226 at 60iterations 0.2941049 8.048508 at 70iterations 0.1637857 4.292831 at 80iterations 9.1150545E-02 2.456029 at 90iterations 5.0594725E-02 1.429169 at 100iterations 2.8011337E-02 0.7158470 at 110iterations 1.5530356E-02 0.3626919 at 120iterations 8.5844593E-03 0.1950378 at 130iterations 4.7357432E-03 0.1126709 at 140iterations 2.6167065E-03 6.4698368E-02 at 150iterations 1.4468376E-03 3.5419464E-02 at 160iterations 7.9948141E-04 1.7527580E-02 at 170iterations 4.4076136E-04 1.0076523E-02 at 180iterations finished qdiffx linear iterations at : 10:31:08 total time elapsed so far: 11.36000 # loops : 180 mean,max change (kT/e) : 4.4076136E-04 1.0076523E-02 energy calculations done at 11.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.55000 DelPhi exited at 10:31:09 11.553u 0.217s 0:12.15 96.7% 0+0k 0+0io 0pf+0w