Tue Oct 11 08:02:36 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 08:02:36 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2563 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5795592 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): -16.60100 44.82500 ymin,ymax (A): -21.78100 36.54300 zmin,zma (A): 34.92600 84.84100 x,y,z range (A): 61.42599 58.32401 49.91500 scale (grids/A): 0.5795592 object centre (A): 14.11200 7.381001 59.88350 number of atom coordinates read : 2563 total number of charged atoms : 2423 net assigned charge : 12.00002 assigned positive charge : 379.2279 centred at (gu) : 90.15723 88.53558 88.05161 assigned negative charge : -367.2285 centred at (gu) : 90.27625 88.49695 88.06345 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5822 nv = 96 ne = 84 npr = 49112 no. pairs analyzed = 49112 no. exposed pairs = 3615 no. arc points = 26371 no. surface atoms = 1206 nbur = 1357 mkacc time = 7.9999998E-02 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 = 1.484000 m= 234 mr = 2695 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3351 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2668 ## 312 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7314 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3660284E-09 1.5310059E-09 midg,1,midg; midg,igrid,midg 2.6193061E-09 2.3375892E-09 1,midg,midg; igrid,midg,midg 4.4976320E-09 4.3966120E-10 gauss-seidel spectral radius is 0.9846151 estimated iterations to convergence 66 setup time was (sec) 0.3700000 now iterating at: 08:02:37 rms-change max change #iterations 9.0695865E-02 15.78837 at 10iterations 6.9359541E-03 1.270187 at 20iterations 5.3930318E-04 0.1035938 at 30iterations 4.2241987E-05 6.8154335E-03 at 40iterations 3.6189945E-06 5.6266785E-04 at 50iterations finished qdiffx linear iterations at : 08:02:40 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 3.6189945E-06 5.6266785E-04 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 08:02:40 3.330u 0.175s 0:03.93 89.0% 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 08:02:40 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2563 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.738678 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): -16.60100 44.82500 ymin,ymax (A): -21.78100 36.54300 zmin,zma (A): 34.92600 84.84100 x,y,z range (A): 61.42599 58.32401 49.91500 scale (grids/A): 1.738678 object centre (A): 14.11200 7.381001 59.88350 number of atom coordinates read : 2563 total number of charged atoms : 2423 net assigned charge : 12.00002 assigned positive charge : 379.2279 centred at (gu) : 90.47104 85.60602 84.15448 assigned negative charge : -367.2285 centred at (gu) : 90.82866 85.49064 84.19011 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63300 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26371 grid for indexing accessible points = 1.400000 m= 19157 mr = 39887 m= 2091 mr = 12783 m= 77 mr = 999 m= 0 mr = 4 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 79 time to turn everything in is 0.3100000 number of dielectric boundary points 30952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 293 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 18820 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) : 0.5795592 object centre at (A) : 14.11200 7.381001 59.88350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9290166E-02 2.1571531E-03 midg,1,midg; midg,igrid,midg 4.8105223E-03 1.4107604E-02 1,midg,midg; igrid,midg,midg 3.5895638E-02 8.8747516E-03 gauss-seidel spectral radius is 0.9983784 estimated iterations to convergence 197 setup time was (sec) 0.5200000 now iterating at: 08:02:41 rms-change max change #iterations 3.442336 161.8543 at 10iterations 1.493169 63.91619 at 20iterations 0.6505558 27.46884 at 30iterations 0.2830642 10.61753 at 40iterations 0.1235247 4.187891 at 50iterations 5.4015953E-02 2.088783 at 60iterations 2.3520475E-02 0.8349838 at 70iterations 1.0256832E-02 0.3860798 at 80iterations 4.4800476E-03 0.1613884 at 90iterations 1.9623928E-03 7.0447922E-02 at 100iterations 8.5388910E-04 2.9160023E-02 at 110iterations 3.7459607E-04 1.2777328E-02 at 120iterations finished qdiffx linear iterations at : 08:02:48 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 3.7459607E-04 1.2777328E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 08:02:48 7.588u 0.196s 0:08.07 96.2% 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 08:02:48 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2563 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.608016 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): -16.60100 44.82500 ymin,ymax (A): -21.78100 36.54300 zmin,zma (A): 34.92600 84.84100 x,y,z range (A): 61.42599 58.32401 49.91500 scale (grids/A): 2.608016 object centre (A): 14.11200 7.381001 59.88350 number of atom coordinates read : 2563 total number of charged atoms : 2423 net assigned charge : 12.00002 assigned positive charge : 379.2279 centred at (gu) : 90.70657 83.40897 81.23153 assigned negative charge : -367.2285 centred at (gu) : 91.24291 83.23600 81.28512 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 146700 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26371 grid for indexing accessible points = 1.400000 m= 64739 mr = 98122 m= 19493 mr = 49885 m= 3381 mr = 14521 m= 282 mr = 2166 m= 8 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 283 time to turn everything in is 0.7700000 number of dielectric boundary points 69775 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 19373 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) : 1.738678 object centre at (A) : 14.11200 7.381001 59.88350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2359828 3.2343497E-03 midg,1,midg; midg,igrid,midg 1.9083921E-02 0.2112669 1,midg,midg; igrid,midg,midg 0.5044836 9.6533008E-02 gauss-seidel spectral radius is 0.9991971 estimated iterations to convergence 279 setup time was (sec) 1.010000 now iterating at: 08:02:50 rms-change max change #iterations 8.672743 364.8809 at 10iterations 4.998406 139.1203 at 20iterations 2.852368 70.70866 at 30iterations 1.620816 43.76539 at 40iterations 0.9200118 19.88669 at 50iterations 0.5208853 13.31102 at 60iterations 0.2932899 6.152878 at 70iterations 0.1652620 3.766708 at 80iterations 9.2716634E-02 2.017426 at 90iterations 5.2221373E-02 1.294167 at 100iterations 2.9307004E-02 0.6817880 at 110iterations 1.6492387E-02 0.3472786 at 120iterations 9.2509380E-03 0.1935349 at 130iterations 5.1907348E-03 0.1113095 at 140iterations 2.9113237E-03 6.3557625E-02 at 150iterations 1.6313386E-03 3.8692951E-02 at 160iterations 9.1770227E-04 1.9920349E-02 at 170iterations 5.1449903E-04 1.0415077E-02 at 180iterations finished qdiffx linear iterations at : 08:03:01 total time elapsed so far: 12.03000 # loops : 180 mean,max change (kT/e) : 5.1449903E-04 1.0415077E-02 energy calculations done at 12.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.16000 DelPhi exited at 08:03:01 12.168u 0.179s 0:12.77 96.5% 0+0k 0+0io 0pf+0w