Sun Oct 9 01:57:27 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 Sun Oct 9 2011 at 01:57:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2434 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: 0.6323156 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): 13.79100 67.68000 ymin,ymax (A): -30.66300 25.63800 zmin,zma (A): 2.448000 46.11300 x,y,z range (A): 53.88900 56.30100 43.66500 scale (grids/A): 0.6323156 object centre (A): 40.73550 -2.512500 24.28050 number of atom coordinates read : 2434 total number of charged atoms : 2299 net assigned charge : 11.50002 assigned positive charge : 356.0542 centred at (gu) : 90.04790 90.74366 89.49709 assigned negative charge : -344.5551 centred at (gu) : 90.08294 90.75437 89.58862 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6903 nv = 96 ne = 84 npr = 47370 no. pairs analyzed = 47370 no. exposed pairs = 3273 no. arc points = 23441 no. surface atoms = 1094 nbur = 1340 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 422 mr = 3626 m= 4 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3660 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2373 ## 223 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8092 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3322912E-08 5.0938738E-09 midg,1,midg; midg,igrid,midg 1.2203231E-08 1.4550483E-08 1,midg,midg; igrid,midg,midg 1.6115379E-08 1.0511960E-08 gauss-seidel spectral radius is 0.9870439 estimated iterations to convergence 72 setup time was (sec) 0.3700000 now iterating at: 01:57:28 rms-change max change #iterations 0.1313429 20.85215 at 10iterations 1.2728753E-02 1.951763 at 20iterations 1.6151498E-03 0.2416534 at 30iterations 4.1323341E-04 7.0528030E-02 at 40iterations 1.4756196E-04 2.5480270E-02 at 50iterations finished qdiffx linear iterations at : 01:57:31 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.4756196E-04 2.5480270E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 01:57:31 3.341u 0.170s 0:03.78 92.8% 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 Sun Oct 9 2011 at 01:57:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2434 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: 1.896947 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): 13.79100 67.68000 ymin,ymax (A): -30.66300 25.63800 zmin,zma (A): 2.448000 46.11300 x,y,z range (A): 53.88900 56.30100 43.66500 scale (grids/A): 1.896947 object centre (A): 40.73550 -2.512500 24.28050 number of atom coordinates read : 2434 total number of charged atoms : 2299 net assigned charge : 11.50002 assigned positive charge : 356.0542 centred at (gu) : 90.14329 92.23059 88.49084 assigned negative charge : -344.5551 centred at (gu) : 90.24876 92.26283 88.76589 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 73977 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23441 grid for indexing accessible points = 1.400000 m= 27533 mr = 49983 m= 4765 mr = 19736 m= 326 mr = 2961 m= 2 mr = 109 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 33814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 18122 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) : 0.6323156 object centre at (A) : 40.73550 -2.512500 24.28050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6820254E-02 -4.5547477E-04 midg,1,midg; midg,igrid,midg 5.1233880E-02 2.9716628E-02 1,midg,midg; igrid,midg,midg 5.7888165E-02 4.7186218E-02 gauss-seidel spectral radius is 0.9986275 estimated iterations to convergence 214 setup time was (sec) 0.5900000 now iterating at: 01:57:32 rms-change max change #iterations 3.959893 169.8862 at 10iterations 1.840879 64.77634 at 20iterations 0.8607891 26.87629 at 30iterations 0.4010707 13.48921 at 40iterations 0.1869628 5.604613 at 50iterations 8.7433904E-02 2.752384 at 60iterations 4.0999070E-02 1.288371 at 70iterations 1.9172350E-02 0.6501808 at 80iterations 9.0586515E-03 0.2808256 at 90iterations 4.3580877E-03 0.1475220 at 100iterations 2.1590879E-03 7.5229645E-02 at 110iterations 1.1261319E-03 4.1015625E-02 at 120iterations finished qdiffx linear iterations at : 01:57:39 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 1.1261319E-03 4.1015625E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 01:57:40 7.718u 0.189s 0:08.26 95.5% 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 Sun Oct 9 2011 at 01:57:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2434 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: 2.845420 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): 13.79100 67.68000 ymin,ymax (A): -30.66300 25.63800 zmin,zma (A): 2.448000 46.11300 x,y,z range (A): 53.88900 56.30100 43.66500 scale (grids/A): 2.845420 object centre (A): 40.73550 -2.512500 24.28050 number of atom coordinates read : 2434 total number of charged atoms : 2299 net assigned charge : 11.50002 assigned positive charge : 356.0542 centred at (gu) : 90.21489 93.34575 87.73621 assigned negative charge : -344.5551 centred at (gu) : 90.37323 93.39425 88.14881 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 170562 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23441 grid for indexing accessible points = 1.400000 m= 86926 mr = 120982 m= 33169 mr = 70070 m= 8664 mr = 26221 m= 1329 mr = 6378 m= 78 mr = 836 m= 0 mr = 21 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9500000 number of dielectric boundary points 76220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 18390 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) : 1.896947 object centre at (A) : 40.73550 -2.512500 24.28050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2787182 -2.4612289E-02 midg,1,midg; midg,igrid,midg 0.7225800 0.3558676 1,midg,midg; igrid,midg,midg 0.6826280 0.5120102 gauss-seidel spectral radius is 0.9992651 estimated iterations to convergence 291 setup time was (sec) 1.170000 now iterating at: 01:57:41 rms-change max change #iterations 9.469393 457.6608 at 10iterations 5.594721 132.3491 at 20iterations 3.269628 75.63431 at 30iterations 1.909517 58.93527 at 40iterations 1.109744 22.41123 at 50iterations 0.6446440 11.97038 at 60iterations 0.3740273 8.671435 at 70iterations 0.2169657 4.951799 at 80iterations 0.1252563 2.486999 at 90iterations 7.2407812E-02 1.410268 at 100iterations 4.1947532E-02 0.7943592 at 110iterations 2.4196252E-02 0.4413166 at 120iterations 1.4002237E-02 0.2783546 at 130iterations 8.1093255E-03 0.1559830 at 140iterations 4.7247065E-03 9.3267441E-02 at 150iterations 2.7699522E-03 5.4658890E-02 at 160iterations 1.6554688E-03 4.2289734E-02 at 170iterations 1.0189153E-03 2.2930145E-02 at 180iterations finished qdiffx linear iterations at : 01:57:52 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 1.0189153E-03 2.2930145E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 01:57:53 12.550u 0.209s 0:13.08 97.4% 0+0k 0+0io 0pf+0w