Mon Oct 10 14:15:08 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 14:15:08 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2790 !!! WARNING: ADP 661 has a net charge of -2.0000 !!! WARNING: MG6 663 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5925137 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): -8.295000 51.78800 ymin,ymax (A): -16.39800 34.48500 zmin,zma (A): 77.69400 131.8210 x,y,z range (A): 60.08300 50.88300 54.12700 scale (grids/A): 0.5925137 object centre (A): 21.74650 9.043498 104.7575 number of atom coordinates read : 2790 total number of charged atoms : 2647 net assigned charge : -4.599987 assigned positive charge : 434.7684 centred at (gu) : 91.95459 89.37713 89.34758 assigned negative charge : -439.3692 centred at (gu) : 91.91466 89.48885 89.38187 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6462 nv = 96 ne = 84 npr = 54890 no. pairs analyzed = 54890 no. exposed pairs = 3834 no. arc points = 26487 no. surface atoms = 1288 nbur = 1502 mkacc time = 0.1000000 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 = 1.456000 m= 338 mr = 3193 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2100000 number of dielectric boundary points 3578 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2715 ## 266 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8154 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4697591E-10 -2.3385840E-09 midg,1,midg; midg,igrid,midg 2.3200908E-09 -4.5686170E-09 1,midg,midg; igrid,midg,midg -1.8652679E-09 -4.1897610E-10 gauss-seidel spectral radius is 0.9852830 estimated iterations to convergence 68 setup time was (sec) 0.4000000 now iterating at: 14:15:09 rms-change max change #iterations 0.1120493 17.38602 at 10iterations 9.0857586E-03 1.624100 at 20iterations 8.4881549E-04 0.1343460 at 30iterations 1.3301002E-04 2.0172119E-02 at 40iterations 3.3393371E-05 4.5738220E-03 at 50iterations finished qdiffx linear iterations at : 14:15:11 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 3.3393371E-05 4.5738220E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 14:15:12 3.410u 0.180s 0:04.15 86.5% 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 Mon Oct 10 2011 at 14:15:12 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2790 !!! WARNING: ADP 661 has a net charge of -2.0000 !!! WARNING: MG6 663 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.777541 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): -8.295000 51.78800 ymin,ymax (A): -16.39800 34.48500 zmin,zma (A): 77.69400 131.8210 x,y,z range (A): 60.08300 50.88300 54.12700 scale (grids/A): 1.777541 object centre (A): 21.74650 9.043498 104.7575 number of atom coordinates read : 2790 total number of charged atoms : 2647 net assigned charge : -4.599987 assigned positive charge : 434.7684 centred at (gu) : 95.86321 88.13071 88.04208 assigned negative charge : -439.3692 centred at (gu) : 95.74363 88.46619 88.14528 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 69214 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26487 grid for indexing accessible points = 1.400000 m= 24266 mr = 45484 m= 3544 mr = 16672 m= 144 mr = 1962 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 136 time to turn everything in is 0.3500000 number of dielectric boundary points 33021 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 189 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 20604 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) : 0.5925137 object centre at (A) : 21.74650 9.043498 104.7575 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7171567E-02 -3.1331878E-02 midg,1,midg; midg,igrid,midg -1.1651989E-03 -1.9963061E-02 1,midg,midg; igrid,midg,midg 1.9892640E-02 2.7737763E-02 gauss-seidel spectral radius is 0.9984656 estimated iterations to convergence 202 setup time was (sec) 0.6000000 now iterating at: 14:15:13 rms-change max change #iterations 3.997046 191.6458 at 10iterations 1.780095 77.68230 at 20iterations 0.7920862 28.74452 at 30iterations 0.3538670 11.85405 at 40iterations 0.1577325 5.344753 at 50iterations 7.0487432E-02 2.454387 at 60iterations 3.1484388E-02 0.9925327 at 70iterations 1.4071590E-02 0.4889832 at 80iterations 6.3314335E-03 0.2076275 at 90iterations 2.8184850E-03 9.5335007E-02 at 100iterations 1.2783168E-03 4.1394711E-02 at 110iterations 5.8153283E-04 1.9176483E-02 at 120iterations finished qdiffx linear iterations at : 14:15:20 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 5.8153283E-04 1.9176483E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 14:15:21 8.006u 0.294s 0:08.69 95.3% 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 14:15:21 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2790 !!! WARNING: ADP 661 has a net charge of -2.0000 !!! WARNING: MG6 663 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.666312 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): -8.295000 51.78800 ymin,ymax (A): -16.39800 34.48500 zmin,zma (A): 77.69400 131.8210 x,y,z range (A): 60.08300 50.88300 54.12700 scale (grids/A): 2.666312 object centre (A): 21.74650 9.043498 104.7575 number of atom coordinates read : 2790 total number of charged atoms : 2647 net assigned charge : -4.599987 assigned positive charge : 434.7684 centred at (gu) : 98.79469 87.19595 87.06287 assigned negative charge : -439.3692 centred at (gu) : 98.61536 87.69924 87.21780 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 159863 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26487 grid for indexing accessible points = 1.400000 m= 78188 mr = 111073 m= 27566 mr = 61187 m= 6218 mr = 21073 m= 679 mr = 4371 m= 17 mr = 353 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 514 time to turn everything in is 0.9200000 number of dielectric boundary points 74474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 21167 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) : 1.777541 object centre at (A) : 21.74650 9.043498 104.7575 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1866147 -0.3932597 midg,1,midg; midg,igrid,midg -3.4591280E-02 -0.2099161 1,midg,midg; igrid,midg,midg 0.4889522 0.3046716 gauss-seidel spectral radius is 0.9992194 estimated iterations to convergence 283 setup time was (sec) 1.190000 now iterating at: 14:15:22 rms-change max change #iterations 9.878285 265.7862 at 10iterations 5.736524 121.5549 at 20iterations 3.306993 76.53767 at 30iterations 1.897488 43.80654 at 40iterations 1.083911 21.83034 at 50iterations 0.6179438 12.20260 at 60iterations 0.3518120 7.285625 at 70iterations 0.1996702 4.099590 at 80iterations 0.1134413 2.391420 at 90iterations 6.4304635E-02 1.243156 at 100iterations 3.6464933E-02 0.6679325 at 110iterations 2.0688461E-02 0.3948922 at 120iterations 1.1713441E-02 0.2674675 at 130iterations 6.6442071E-03 0.1301479 at 140iterations 3.7782826E-03 8.2221985E-02 at 150iterations 2.1528928E-03 4.5486450E-02 at 160iterations 1.2330052E-03 2.4088383E-02 at 170iterations 7.1722898E-04 1.5351534E-02 at 180iterations finished qdiffx linear iterations at : 14:15:34 total time elapsed so far: 13.23000 # loops : 180 mean,max change (kT/e) : 7.1722898E-04 1.5351534E-02 energy calculations done at 13.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.37000 DelPhi exited at 14:15:35 13.369u 0.289s 0:14.36 94.9% 0+0k 0+0io 0pf+0w