Sun Oct 9 13:20:22 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 Sun Oct 9 2011 at 13:20:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 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: 0.6788452 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): -6.971000 44.56600 ymin,ymax (A): 22.15500 74.59700 zmin,zma (A): 40.55900 84.33200 x,y,z range (A): 51.53700 52.44200 43.77300 scale (grids/A): 0.6788452 object centre (A): 18.79750 48.37600 62.44550 number of atom coordinates read : 2393 total number of charged atoms : 2251 net assigned charge : 3.500024 assigned positive charge : 365.4110 centred at (gu) : 89.83764 90.80435 90.79976 assigned negative charge : -361.9116 centred at (gu) : 89.83184 90.98053 90.87669 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7421 nv = 96 ne = 84 npr = 48314 no. pairs analyzed = 48314 no. exposed pairs = 3037 no. arc points = 21163 no. surface atoms = 1015 nbur = 1378 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 472 mr = 4088 m= 4 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2051 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8543 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2188865E-08 -9.0451557E-09 midg,1,midg; midg,igrid,midg 5.6299694E-08 -4.4559091E-08 1,midg,midg; igrid,midg,midg 1.4059755E-08 1.6503488E-08 gauss-seidel spectral radius is 0.9887287 estimated iterations to convergence 77 setup time was (sec) 0.5300000 now iterating at: 13:20:23 rms-change max change #iterations 0.1833838 27.61577 at 10iterations 2.1032896E-02 2.953770 at 20iterations 2.7525667E-03 0.3913994 at 30iterations 5.8041315E-04 8.9370728E-02 at 40iterations 1.8098869E-04 2.8202057E-02 at 50iterations finished qdiffx linear iterations at : 13:20:26 total time elapsed so far: 3.680000 # loops : 50 mean,max change (kT/e) : 1.8098869E-04 2.8202057E-02 energy calculations done at 3.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.870000 DelPhi exited at 13:20:27 3.873u 0.181s 0:04.33 93.5% 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 Sun Oct 9 2011 at 13:20:27 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 = 2393 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: 2.036536 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): -6.971000 44.56600 ymin,ymax (A): 22.15500 74.59700 zmin,zma (A): 40.55900 84.33200 x,y,z range (A): 51.53700 52.44200 43.77300 scale (grids/A): 2.036536 object centre (A): 18.79750 48.37600 62.44550 number of atom coordinates read : 2393 total number of charged atoms : 2251 net assigned charge : 3.500024 assigned positive charge : 365.4110 centred at (gu) : 89.51223 92.41279 92.39883 assigned negative charge : -361.9116 centred at (gu) : 89.49515 92.94135 92.62995 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 78210 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21163 grid for indexing accessible points = 1.400000 m= 29810 mr = 53775 m= 5388 mr = 21985 m= 473 mr = 3443 m= 6 mr = 241 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 300 time to turn everything in is 0.6000000 number of dielectric boundary points 34443 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17821 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) : 0.6788452 object centre at (A) : 18.79750 48.37600 62.44550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3059748E-02 -1.8225385E-04 midg,1,midg; midg,igrid,midg 1.7351007E-02 -6.4489469E-02 1,midg,midg; igrid,midg,midg 4.2671137E-02 7.6424256E-03 gauss-seidel spectral radius is 0.9987812 estimated iterations to convergence 227 setup time was (sec) 0.9300000 now iterating at: 13:20:28 rms-change max change #iterations 4.641052 268.0932 at 10iterations 2.249035 72.52565 at 20iterations 1.099683 40.76460 at 30iterations 0.5382635 18.78494 at 40iterations 0.2631250 8.027238 at 50iterations 0.1282376 4.172115 at 60iterations 6.2850460E-02 1.920514 at 70iterations 3.0856112E-02 0.9387851 at 80iterations 1.5186722E-02 0.4471931 at 90iterations 7.5116288E-03 0.2110634 at 100iterations 3.7661772E-03 0.1335945 at 110iterations 1.9436526E-03 5.9494019E-02 at 120iterations finished qdiffx linear iterations at : 13:20:35 total time elapsed so far: 8.090000 # loops : 120 mean,max change (kT/e) : 1.9436526E-03 5.9494019E-02 energy calculations done at 8.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.290000 DelPhi exited at 13:20:35 8.290u 0.267s 0:08.82 96.9% 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 Sun Oct 9 2011 at 13:20:35 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 = 2393 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: 3.054803 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): -6.971000 44.56600 ymin,ymax (A): 22.15500 74.59700 zmin,zma (A): 40.55900 84.33200 x,y,z range (A): 51.53700 52.44200 43.77300 scale (grids/A): 3.054803 object centre (A): 18.79750 48.37600 62.44550 number of atom coordinates read : 2393 total number of charged atoms : 2251 net assigned charge : 3.500024 assigned positive charge : 365.4110 centred at (gu) : 89.26821 93.61906 93.59804 assigned negative charge : -361.9116 centred at (gu) : 89.24274 94.41193 93.94489 start vw surface at 0.1400000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 180493 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21163 grid for indexing accessible points = 1.400000 m= 94070 mr = 130504 m= 36727 mr = 76697 m= 9857 mr = 29509 m= 1916 mr = 7431 m= 231 mr = 1389 m= 6 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 874 time to turn everything in is 1.600000 number of dielectric boundary points 77635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 18008 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) : 2.036536 object centre at (A) : 18.79750 48.37600 62.44550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4283232 -0.1275578 midg,1,midg; midg,igrid,midg 0.3809602 -0.6997262 1,midg,midg; igrid,midg,midg 0.4602739 -0.1610052 gauss-seidel spectral radius is 0.9992875 estimated iterations to convergence 296 setup time was (sec) 1.940000 now iterating at: 13:20:38 rms-change max change #iterations 10.63118 423.0815 at 10iterations 6.281009 136.4034 at 20iterations 3.706443 82.11485 at 30iterations 2.180632 44.55846 at 40iterations 1.282251 22.87531 at 50iterations 0.7507313 15.07521 at 60iterations 0.4392930 8.001072 at 70iterations 0.2574056 4.847343 at 80iterations 0.1500649 2.874399 at 90iterations 8.7540224E-02 1.590572 at 100iterations 5.1257469E-02 0.8418808 at 110iterations 3.0024383E-02 0.5152121 at 120iterations 1.7682301E-02 0.3229237 at 130iterations 1.0454236E-02 0.2189407 at 140iterations 6.3354126E-03 0.1133738 at 150iterations 3.9520985E-03 7.9353333E-02 at 160iterations 2.5775346E-03 5.2532196E-02 at 170iterations 1.7878108E-03 4.1530609E-02 at 180iterations finished qdiffx linear iterations at : 13:20:49 total time elapsed so far: 13.81000 # loops : 180 mean,max change (kT/e) : 1.7878108E-03 4.1530609E-02 energy calculations done at 13.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.00000 DelPhi exited at 13:20:50 13.998u 0.288s 0:14.62 97.6% 0+0k 0+0io 0pf+0w