Tue Oct 11 06:49:21 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 Tue Oct 11 2011 at 06:49:21 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 = 2942 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: 0.5573735 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): -20.75700 43.11400 ymin,ymax (A): 21.92600 78.75300 zmin,zma (A): -71.24700 -22.49100 x,y,z range (A): 63.87100 56.82700 48.75600 scale (grids/A): 0.5573735 object centre (A): 11.17850 50.33950 -46.86900 number of atom coordinates read : 2942 total number of charged atoms : 2803 net assigned charge : -0.4999959 assigned positive charge : 427.3497 centred at (gu) : 90.09113 89.88766 89.29937 assigned negative charge : -427.8503 centred at (gu) : 90.08855 89.97932 89.29250 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6094 nv = 96 ne = 84 npr = 59885 no. pairs analyzed = 59885 no. exposed pairs = 3685 no. arc points = 26096 no. surface atoms = 1256 nbur = 1686 mkacc time = 0.1400000 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 = 1.540000 m= 263 mr = 3231 m= 0 mr = 17 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2615 ## 297 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7809 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3666397E-10 1.5057740E-11 midg,1,midg; midg,igrid,midg 8.5527768E-10 -9.2289049E-10 1,midg,midg; igrid,midg,midg -7.1814513E-11 -2.3943660E-11 gauss-seidel spectral radius is 0.9833987 estimated iterations to convergence 64 setup time was (sec) 0.5900000 now iterating at: 06:49:21 rms-change max change #iterations 8.0709167E-02 13.70243 at 10iterations 5.7369289E-03 1.011497 at 20iterations 4.0750048E-04 5.9993744E-02 at 30iterations 2.9038076E-05 4.7302246E-03 at 40iterations 2.3008897E-06 4.0435791E-04 at 50iterations finished qdiffx linear iterations at : 06:49:25 total time elapsed so far: 4.110000 # loops : 50 mean,max change (kT/e) : 2.3008897E-06 4.0435791E-04 energy calculations done at 4.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 06:49:26 4.323u 0.272s 0:05.07 90.5% 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 Tue Oct 11 2011 at 06:49:26 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 = 2942 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: 1.672120 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): -20.75700 43.11400 ymin,ymax (A): 21.92600 78.75300 zmin,zma (A): -71.24700 -22.49100 x,y,z range (A): 63.87100 56.82700 48.75600 scale (grids/A): 1.672120 object centre (A): 11.17850 50.33950 -46.86900 number of atom coordinates read : 2942 total number of charged atoms : 2803 net assigned charge : -0.4999959 assigned positive charge : 427.3497 centred at (gu) : 90.27284 89.66238 87.89780 assigned negative charge : -427.8503 centred at (gu) : 90.26527 89.93761 87.87704 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 66568 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26096 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 22264 mr = 45372 m= 2500 mr = 15886 m= 61 mr = 1351 m= 0 mr = 6 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 28778 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 277 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6100000 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) : 0.5573735 object centre at (A) : 11.17850 50.33950 -46.86900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9170082E-03 1.0516843E-02 midg,1,midg; midg,igrid,midg -3.2407185E-03 4.9213297E-03 1,midg,midg; igrid,midg,midg 4.5501548E-03 -8.0106249E-03 gauss-seidel spectral radius is 0.9982768 estimated iterations to convergence 191 setup time was (sec) 0.7800000 now iterating at: 06:49:27 rms-change max change #iterations 3.429541 187.1726 at 10iterations 1.456677 71.16286 at 20iterations 0.6223545 23.05485 at 30iterations 0.2653722 9.107265 at 40iterations 0.1137453 4.369083 at 50iterations 4.8395123E-02 1.683832 at 60iterations 2.0592850E-02 0.7636871 at 70iterations 8.8282945E-03 0.3183594 at 80iterations 3.7499892E-03 0.1369562 at 90iterations 1.6052702E-03 6.1790466E-02 at 100iterations 6.8369444E-04 2.4508476E-02 at 110iterations 2.9337712E-04 1.0909557E-02 at 120iterations finished qdiffx linear iterations at : 06:49:33 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 2.9337712E-04 1.0909557E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 06:49:34 7.702u 0.262s 0:08.39 94.8% 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 06:49:34 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 = 2942 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: 2.508180 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): -20.75700 43.11400 ymin,ymax (A): 21.92600 78.75300 zmin,zma (A): -71.24700 -22.49100 x,y,z range (A): 63.87100 56.82700 48.75600 scale (grids/A): 2.508180 object centre (A): 11.17850 50.33950 -46.86900 number of atom coordinates read : 2942 total number of charged atoms : 2803 net assigned charge : -0.4999959 assigned positive charge : 427.3497 centred at (gu) : 90.40924 89.49342 86.84645 assigned negative charge : -427.8503 centred at (gu) : 90.39787 89.90641 86.81555 start vw surface at 0.1600000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 154303 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26096 grid for indexing accessible points = 1.400000 m= 74569 mr = 110531 m= 23551 mr = 60018 m= 4155 mr = 18288 m= 292 mr = 2893 m= 2 mr = 156 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.130000 number of dielectric boundary points 64986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 22407 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) : 1.672120 object centre at (A) : 11.17850 50.33950 -46.86900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5130334E-02 0.1739001 midg,1,midg; midg,igrid,midg -4.5021754E-02 7.1879208E-02 1,midg,midg; igrid,midg,midg -1.4797290E-02 -0.1395168 gauss-seidel spectral radius is 0.9991680 estimated iterations to convergence 274 setup time was (sec) 1.420000 now iterating at: 06:49:36 rms-change max change #iterations 8.692221 368.2904 at 10iterations 4.921709 144.6527 at 20iterations 2.772697 59.11275 at 30iterations 1.556388 32.21262 at 40iterations 0.8737369 18.12490 at 50iterations 0.4866293 10.63745 at 60iterations 0.2718963 6.093820 at 70iterations 0.1513913 3.115325 at 80iterations 8.4336288E-02 1.618069 at 90iterations 4.6740066E-02 1.022992 at 100iterations 2.6073502E-02 0.5010810 at 110iterations 1.4483009E-02 0.2760768 at 120iterations 8.0329813E-03 0.1522141 at 130iterations 4.4699176E-03 9.1529846E-02 at 140iterations 2.4732535E-03 5.0762177E-02 at 150iterations 1.3800159E-03 2.7899146E-02 at 160iterations 7.6428428E-04 1.5994415E-02 at 170iterations 4.2368800E-04 8.0575943E-03 at 180iterations finished qdiffx linear iterations at : 06:49:46 total time elapsed so far: 11.76000 # loops : 180 mean,max change (kT/e) : 4.2368800E-04 8.0575943E-03 energy calculations done at 11.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.96000 DelPhi exited at 06:49:47 11.962u 0.263s 0:13.05 93.6% 0+0k 0+0io 0pf+0w