Sun Oct 9 12:36:03 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 Sun Oct 9 2011 at 12:36:03 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 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: 0.7046295 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): -6.076000 43.88200 ymin,ymax (A): -14.37200 36.15100 zmin,zma (A): 0.8210000 45.40300 x,y,z range (A): 49.95800 50.52300 44.58200 scale (grids/A): 0.7046295 object centre (A): 18.90300 10.88950 23.11200 number of atom coordinates read : 2383 total number of charged atoms : 2242 net assigned charge : 4.500021 assigned positive charge : 365.3711 centred at (gu) : 89.62292 91.28017 90.85723 assigned negative charge : -360.8716 centred at (gu) : 89.61948 91.44451 90.93494 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8038 nv = 96 ne = 84 npr = 47831 no. pairs analyzed = 47831 no. exposed pairs = 2993 no. arc points = 21142 no. surface atoms = 997 nbur = 1386 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 489 mr = 4477 m= 5 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 71 time to turn everything in is 0.1900000 number of dielectric boundary points 3979 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1939 ## 179 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8941 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6471337E-08 -6.0609207E-09 midg,1,midg; midg,igrid,midg 9.6386771E-08 -6.8427866E-08 1,midg,midg; igrid,midg,midg 3.7970405E-08 3.6363055E-08 gauss-seidel spectral radius is 0.9895345 estimated iterations to convergence 80 setup time was (sec) 0.3800000 now iterating at: 12:36:04 rms-change max change #iterations 0.2133243 34.78659 at 10iterations 2.6875064E-02 3.864246 at 20iterations 3.8566780E-03 0.4697914 at 30iterations 9.2084921E-04 0.1453495 at 40iterations 3.1565517E-04 5.3569794E-02 at 50iterations finished qdiffx linear iterations at : 12:36:07 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 3.1565517E-04 5.3569794E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 12:36:07 3.398u 0.169s 0:03.84 92.4% 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 Sun Oct 9 2011 at 12:36:07 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 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: 2.113889 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): -6.076000 43.88200 ymin,ymax (A): -14.37200 36.15100 zmin,zma (A): 0.8210000 45.40300 x,y,z range (A): 49.95800 50.52300 44.58200 scale (grids/A): 2.113889 object centre (A): 18.90300 10.88950 23.11200 number of atom coordinates read : 2383 total number of charged atoms : 2242 net assigned charge : 4.500021 assigned positive charge : 365.3711 centred at (gu) : 88.86850 93.83996 92.57132 assigned negative charge : -360.8716 centred at (gu) : 88.85828 94.33334 92.80450 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 84756 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21142 grid for indexing accessible points = 1.400000 m= 33063 mr = 58913 m= 6098 mr = 24770 m= 570 mr = 4039 m= 5 mr = 294 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 874 time to turn everything in is 0.4200000 number of dielectric boundary points 36476 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 99 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 17795 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) : 0.7046295 object centre at (A) : 18.90300 10.88950 23.11200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3015968E-02 2.5279930E-02 midg,1,midg; midg,igrid,midg 1.6356567E-02 -5.9491847E-02 1,midg,midg; igrid,midg,midg 6.3740671E-02 -3.6989911E-03 gauss-seidel spectral radius is 0.9988590 estimated iterations to convergence 234 setup time was (sec) 0.6500000 now iterating at: 12:36:08 rms-change max change #iterations 5.028162 194.5213 at 10iterations 2.493899 83.45903 at 20iterations 1.243118 36.37347 at 30iterations 0.6212672 18.45786 at 40iterations 0.3104635 9.429153 at 50iterations 0.1550002 4.416824 at 60iterations 7.7978246E-02 2.169438 at 70iterations 3.8996145E-02 1.103970 at 80iterations 1.9719271E-02 0.5448775 at 90iterations 1.0069325E-02 0.2986298 at 100iterations 5.2219583E-03 0.1648216 at 110iterations 2.8057331E-03 8.7772369E-02 at 120iterations finished qdiffx linear iterations at : 12:36:15 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 2.8057331E-03 8.7772369E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 12:36:16 7.941u 0.190s 0:08.40 96.7% 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 Sun Oct 9 2011 at 12:36:16 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 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: 3.170833 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): -6.076000 43.88200 ymin,ymax (A): -14.37200 36.15100 zmin,zma (A): 0.8210000 45.40300 x,y,z range (A): 49.95800 50.52300 44.58200 scale (grids/A): 3.170833 object centre (A): 18.90300 10.88950 23.11200 number of atom coordinates read : 2383 total number of charged atoms : 2242 net assigned charge : 4.500021 assigned positive charge : 365.3711 centred at (gu) : 88.30260 95.75983 93.85683 assigned negative charge : -360.8716 centred at (gu) : 88.28751 96.49992 94.20678 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 195358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21142 grid for indexing accessible points = 1.400000 m= 103601 mr = 142203 m= 41112 mr = 85408 m= 11341 mr = 33637 m= 2318 mr = 8802 m= 312 mr = 1646 m= 6 mr = 203 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 2893 time to turn everything in is 1.290000 number of dielectric boundary points 82149 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 17932 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) : 2.113889 object centre at (A) : 18.90300 10.88950 23.11200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5205286 0.1156102 midg,1,midg; midg,igrid,midg 0.3037373 -0.6807695 1,midg,midg; igrid,midg,midg 0.7768879 -0.3305702 gauss-seidel spectral radius is 0.9993063 estimated iterations to convergence 300 setup time was (sec) 1.520000 now iterating at: 12:36:17 rms-change max change #iterations 11.13844 430.1256 at 10iterations 6.612934 135.4459 at 20iterations 3.911504 72.05214 at 30iterations 2.313420 41.59927 at 40iterations 1.366342 26.13725 at 50iterations 0.8047634 13.06064 at 60iterations 0.4727522 7.847044 at 70iterations 0.2783432 5.167334 at 80iterations 0.1637064 2.664280 at 90iterations 9.6324205E-02 1.617615 at 100iterations 5.6799684E-02 0.9289036 at 110iterations 3.3638380E-02 0.6198425 at 120iterations 2.0091722E-02 0.3619480 at 130iterations 1.2188422E-02 0.2575073 at 140iterations 7.6723252E-03 0.1451797 at 150iterations 5.0550126E-03 0.1027679 at 160iterations 3.5520233E-03 7.1834564E-02 at 170iterations 2.6634126E-03 5.6795120E-02 at 180iterations finished qdiffx linear iterations at : 12:36:30 total time elapsed so far: 14.25000 # loops : 180 mean,max change (kT/e) : 2.6634126E-03 5.6795120E-02 energy calculations done at 14.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.38000 DelPhi exited at 12:36:31 14.383u 0.226s 0:14.86 98.2% 0+0k 0+0io 0pf+0w