Tue Oct 11 03:20:06 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 03:20:06 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1923 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7136700 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): 18.71400 64.56700 ymin,ymax (A): -11.03100 35.21700 zmin,zma (A): 0.3909999 50.27400 x,y,z range (A): 45.85300 46.24800 49.88300 scale (grids/A): 0.7136700 object centre (A): 41.64050 12.09300 25.33250 number of atom coordinates read : 1923 total number of charged atoms : 1756 net assigned charge : 5.000005 assigned positive charge : 287.1209 centred at (gu) : 91.11155 89.72140 90.64456 assigned negative charge : -282.1212 centred at (gu) : 91.12747 90.03584 90.80041 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6788 nv = 96 ne = 84 npr = 37128 no. pairs analyzed = 37128 no. exposed pairs = 2554 no. arc points = 18180 no. surface atoms = 862 nbur = 1061 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 461 mr = 3642 m= 2 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 60 time to turn everything in is 0.1600000 number of dielectric boundary points 3541 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1565 ## 135 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7117 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1296091E-07 -3.6620779E-08 midg,1,midg; midg,igrid,midg 2.1697572E-07 -1.1052786E-07 1,midg,midg; igrid,midg,midg 4.6651529E-08 5.0505857E-08 gauss-seidel spectral radius is 0.9897572 estimated iterations to convergence 80 setup time was (sec) 0.3500000 now iterating at: 03:20:06 rms-change max change #iterations 0.1965498 27.06634 at 10iterations 2.4844270E-02 4.033734 at 20iterations 3.0581027E-03 0.4113121 at 30iterations 3.8467100E-04 5.0964355E-02 at 40iterations 4.6774334E-05 6.5536499E-03 at 50iterations finished qdiffx linear iterations at : 03:20:09 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 4.6774334E-05 6.5536499E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 03:20:10 3.330u 0.169s 0:03.88 89.9% 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 03:20:10 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1923 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.141010 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): 18.71400 64.56700 ymin,ymax (A): -11.03100 35.21700 zmin,zma (A): 0.3909999 50.27400 x,y,z range (A): 45.85300 46.24800 49.88300 scale (grids/A): 2.141010 object centre (A): 41.64050 12.09300 25.33250 number of atom coordinates read : 1923 total number of charged atoms : 1756 net assigned charge : 5.000005 assigned positive charge : 287.1209 centred at (gu) : 93.33479 89.16404 91.93363 assigned negative charge : -282.1212 centred at (gu) : 93.38251 90.10753 92.40140 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71156 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18180 grid for indexing accessible points = 1.400000 m= 28062 mr = 47922 m= 5384 mr = 21028 m= 491 mr = 3339 m= 12 mr = 230 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1758 time to turn everything in is 0.3700000 number of dielectric boundary points 32586 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 13942 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) : 0.7136700 object centre at (A) : 41.64050 12.09300 25.33250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3046642E-02 -1.9218370E-02 midg,1,midg; midg,igrid,midg 7.5081289E-02 -8.5187189E-02 1,midg,midg; igrid,midg,midg 1.3809927E-02 5.5748031E-02 gauss-seidel spectral radius is 0.9988396 estimated iterations to convergence 232 setup time was (sec) 0.5800000 now iterating at: 03:20:11 rms-change max change #iterations 4.489284 225.1165 at 10iterations 2.219914 82.06761 at 20iterations 1.102527 35.63919 at 30iterations 0.5480971 17.94565 at 40iterations 0.2716955 8.109375 at 50iterations 0.1344502 4.354038 at 60iterations 6.6898525E-02 2.167257 at 70iterations 3.3162944E-02 0.9835281 at 80iterations 1.6496386E-02 0.5428972 at 90iterations 8.1719877E-03 0.2544987 at 100iterations 4.0490064E-03 0.1397076 at 110iterations 2.0184873E-03 6.2690735E-02 at 120iterations finished qdiffx linear iterations at : 03:20:18 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 2.0184873E-03 6.2690735E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 03:20:18 7.794u 0.188s 0:08.41 94.7% 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 03:20:18 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1923 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.211515 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): 18.71400 64.56700 ymin,ymax (A): -11.03100 35.21700 zmin,zma (A): 0.3909999 50.27400 x,y,z range (A): 45.85300 46.24800 49.88300 scale (grids/A): 3.211515 object centre (A): 41.64050 12.09300 25.33250 number of atom coordinates read : 1923 total number of charged atoms : 1756 net assigned charge : 5.000005 assigned positive charge : 287.1209 centred at (gu) : 95.00226 88.74607 92.90052 assigned negative charge : -282.1212 centred at (gu) : 95.07375 90.16131 93.60209 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 163697 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18180 grid for indexing accessible points = 1.400000 m= 86448 mr = 115818 m= 35724 mr = 70908 m= 9995 mr = 29080 m= 1988 mr = 7360 m= 214 mr = 1386 m= 5 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 5882 time to turn everything in is 1.100000 number of dielectric boundary points 73414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 14047 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) : 2.141010 object centre at (A) : 41.64050 12.09300 25.33250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4302317 -0.2381321 midg,1,midg; midg,igrid,midg 0.4801444 -0.9635267 1,midg,midg; igrid,midg,midg 8.5022397E-02 0.6185222 gauss-seidel spectral radius is 0.9993131 estimated iterations to convergence 301 setup time was (sec) 1.330000 now iterating at: 03:20:20 rms-change max change #iterations 10.09971 356.5462 at 10iterations 6.020483 124.4505 at 20iterations 3.573010 70.42607 at 30iterations 2.113347 39.65936 at 40iterations 1.248536 23.16974 at 50iterations 0.7361690 13.45195 at 60iterations 0.4327609 8.649490 at 70iterations 0.2545747 5.047836 at 80iterations 0.1494577 2.773564 at 90iterations 8.7714270E-02 1.553548 at 100iterations 5.1490273E-02 0.9088821 at 110iterations 3.0220421E-02 0.5359783 at 120iterations 1.7687591E-02 0.3163261 at 130iterations 1.0383843E-02 0.1831627 at 140iterations 6.0796589E-03 0.1049118 at 150iterations 3.5672900E-03 6.1503887E-02 at 160iterations 2.0889377E-03 3.3672333E-02 at 170iterations 1.2257374E-03 2.2209167E-02 at 180iterations finished qdiffx linear iterations at : 03:20:31 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 1.2257374E-03 2.2209167E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.53000 DelPhi exited at 03:20:31 12.535u 0.210s 0:13.14 96.9% 0+0k 0+0io 0pf+0w