Mon Oct 10 14:20:45 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 Mon Oct 10 2011 at 14:20:45 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4256 !!! WARNING: ADP 663 has a net charge of -2.0000 !!! WARNING: ADP 664 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.4897106 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): -1.726000 51.26800 ymin,ymax (A): -21.32600 41.52600 zmin,zma (A): -19.29200 53.40400 x,y,z range (A): 52.99400 62.85200 72.69600 scale (grids/A): 0.4897106 object centre (A): 24.77100 10.10000 17.05600 number of atom coordinates read : 4256 total number of charged atoms : 4097 net assigned charge : -10.99998 assigned positive charge : 670.2847 centred at (gu) : 89.01233 89.92323 89.35506 assigned negative charge : -681.2885 centred at (gu) : 89.07193 89.97001 89.40018 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6599 nv = 96 ne = 84 npr = 80567 no. pairs analyzed = 80567 no. exposed pairs = 6426 no. arc points = 44233 no. surface atoms = 2116 nbur = 2140 mkacc time = 0.2400000 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 = 1.736000 m= 264 mr = 2890 m= 0 mr = 2 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 3971 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4207 ## 694 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 8862 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9020677E-11 -8.7600253E-11 midg,1,midg; midg,igrid,midg -1.4995607E-11 -1.0375255E-10 1,midg,midg; igrid,midg,midg -2.2937756E-12 -9.0786469E-11 gauss-seidel spectral radius is 0.9786632 estimated iterations to convergence 57 setup time was (sec) 0.7900000 now iterating at: 14:20:46 rms-change max change #iterations 5.1233646E-02 9.767378 at 10iterations 3.8830559E-03 0.5655251 at 20iterations 1.1839942E-03 0.1598225 at 30iterations 4.5748791E-04 6.1803818E-02 at 40iterations 1.7765201E-04 2.3986816E-02 at 50iterations finished qdiffx linear iterations at : 14:20:52 total time elapsed so far: 6.570000 # loops : 50 mean,max change (kT/e) : 1.7765201E-04 2.3986816E-02 energy calculations done at 6.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.750000 DelPhi exited at 14:20:53 6.759u 0.521s 0:07.59 95.7% 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 Mon Oct 10 2011 at 14:20:53 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4256 !!! WARNING: ADP 663 has a net charge of -2.0000 !!! WARNING: ADP 664 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.469132 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): -1.726000 51.26800 ymin,ymax (A): -21.32600 41.52600 zmin,zma (A): -19.29200 53.40400 x,y,z range (A): 52.99400 62.85200 72.69600 scale (grids/A): 1.469132 object centre (A): 24.77100 10.10000 17.05600 number of atom coordinates read : 4256 total number of charged atoms : 4097 net assigned charge : -10.99998 assigned positive charge : 670.2847 centred at (gu) : 87.03569 89.76855 88.06364 assigned negative charge : -681.2885 centred at (gu) : 87.21542 89.90954 88.19996 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 73960 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44233 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 20463 mr = 46645 m= 1636 mr = 11916 m= 22 mr = 494 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7700000 number of dielectric boundary points 37026 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 552 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 30307 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) : 0.4897106 object centre at (A) : 24.77100 10.10000 17.05600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0613708E-03 2.1120257E-04 midg,1,midg; midg,igrid,midg 1.1566073E-05 -1.7734533E-03 1,midg,midg; igrid,midg,midg -4.3204208E-03 -9.6178623E-03 gauss-seidel spectral radius is 0.9978940 estimated iterations to convergence 173 setup time was (sec) 1.290000 now iterating at: 14:20:55 rms-change max change #iterations 3.361018 165.2725 at 10iterations 1.298606 52.72182 at 20iterations 0.5047901 19.00779 at 30iterations 0.1963968 7.323135 at 40iterations 7.6700933E-02 2.963750 at 50iterations 3.0204326E-02 1.077071 at 60iterations 1.2075484E-02 0.4679737 at 70iterations 5.0670472E-03 0.1988831 at 80iterations 2.3935437E-03 8.8465691E-02 at 90iterations 1.3174241E-03 4.2314529E-02 at 100iterations 8.2881871E-04 2.4513245E-02 at 110iterations 5.5670820E-04 1.5289307E-02 at 120iterations finished qdiffx linear iterations at : 14:21:13 total time elapsed so far: 19.38000 # loops : 120 mean,max change (kT/e) : 5.5670820E-04 1.5289307E-02 energy calculations done at 19.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.56000 DelPhi exited at 14:21:14 19.566u 0.822s 0:20.83 97.8% 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 Mon Oct 10 2011 at 14:21:14 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4256 !!! WARNING: ADP 663 has a net charge of -2.0000 !!! WARNING: ADP 664 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.203698 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): -1.726000 51.26800 ymin,ymax (A): -21.32600 41.52600 zmin,zma (A): -19.29200 53.40400 x,y,z range (A): 52.99400 62.85200 72.69600 scale (grids/A): 2.203698 object centre (A): 24.77100 10.10000 17.05600 number of atom coordinates read : 4256 total number of charged atoms : 4097 net assigned charge : -10.99998 assigned positive charge : 670.2847 centred at (gu) : 85.55287 89.65241 87.09506 assigned negative charge : -681.2885 centred at (gu) : 85.82318 89.86423 87.29965 start vw surface at 0.1600000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 171935 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44233 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 73040 mr = 116146 m= 17435 mr = 52590 m= 2006 mr = 11050 m= 60 mr = 939 m= 0 mr = 4 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.840000 number of dielectric boundary points 83747 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 102 iepsmp to db, and charging done at 2.090000 number of grid points assigned charge 32648 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) : 1.469132 object centre at (A) : 24.77100 10.10000 17.05600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.6885949E-02 4.8498906E-02 midg,1,midg; midg,igrid,midg 1.7411228E-02 5.4831780E-03 1,midg,midg; igrid,midg,midg -6.8508789E-02 -0.1676046 gauss-seidel spectral radius is 0.9990968 estimated iterations to convergence 263 setup time was (sec) 2.450000 now iterating at: 14:21:17 rms-change max change #iterations 9.717428 277.0964 at 10iterations 5.563489 155.6353 at 20iterations 3.144153 85.13021 at 30iterations 1.763946 45.79625 at 40iterations 0.9832790 27.61795 at 50iterations 0.5427232 13.21377 at 60iterations 0.3005911 7.978439 at 70iterations 0.1647767 3.889778 at 80iterations 9.0522006E-02 2.217239 at 90iterations 4.9586140E-02 1.140137 at 100iterations 2.7119348E-02 0.6836567 at 110iterations 1.4807986E-02 0.3143320 at 120iterations 8.1108790E-03 0.1900291 at 130iterations 4.4483328E-03 9.5619202E-02 at 140iterations 2.4564927E-03 5.6417465E-02 at 150iterations 1.3737773E-03 3.0951500E-02 at 160iterations 7.8888709E-04 1.7234802E-02 at 170iterations 4.7035722E-04 1.0541916E-02 at 180iterations finished qdiffx linear iterations at : 14:21:37 total time elapsed so far: 21.90000 # loops : 180 mean,max change (kT/e) : 4.7035722E-04 1.0541916E-02 energy calculations done at 21.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.07000 DelPhi exited at 14:21:37 22.077u 1.006s 0:23.62 97.6% 0+0k 0+0io 0pf+0w