Sun Oct 16 15:12:53 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 16 2011 at 15:12:53 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2746 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: SEP 228 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6781340 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): -5.973000 41.99700 ymin,ymax (A): -3.583000 48.70700 zmin,zma (A): 41.00600 93.50300 x,y,z range (A): 47.97000 52.29000 52.49700 scale (grids/A): 0.6781340 object centre (A): 18.01200 22.56200 67.25450 number of atom coordinates read : 2746 total number of charged atoms : 2597 net assigned charge : 5.039016 assigned positive charge : 421.2159 centred at (gu) : 90.48885 91.78307 90.76875 assigned negative charge : -416.1772 centred at (gu) : 90.17521 91.60231 90.84856 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8490 nv = 96 ne = 84 npr = 56151 no. pairs analyzed = 56151 no. exposed pairs = 3332 no. arc points = 23177 no. surface atoms = 1121 nbur = 1625 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 530 mr = 4917 m= 2 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 135 time to turn everything in is 0.3200000 number of dielectric boundary points 4038 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2178 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9829 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9070674E-08 -8.9940340E-09 midg,1,midg; midg,igrid,midg -2.8784184E-08 1.1307278E-07 1,midg,midg; igrid,midg,midg -7.9819422E-08 1.3294328E-07 gauss-seidel spectral radius is 0.9887368 estimated iterations to convergence 77 setup time was (sec) 0.5500000 now iterating at: 15:12:54 rms-change max change #iterations 0.1989352 25.11798 at 10iterations 2.3115806E-02 3.090302 at 20iterations 2.7594927E-03 0.3626022 at 30iterations 4.2232929E-04 5.8677673E-02 at 40iterations 9.9221346E-05 1.3816833E-02 at 50iterations finished qdiffx linear iterations at : 15:12:57 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 9.9221346E-05 1.3816833E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 15:12:57 3.447u 0.170s 0:03.91 92.3% 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 Sun Oct 16 2011 at 15:12:57 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2746 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: SEP 228 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.034402 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): -5.973000 41.99700 ymin,ymax (A): -3.583000 48.70700 zmin,zma (A): 41.00600 93.50300 x,y,z range (A): 47.97000 52.29000 52.49700 scale (grids/A): 2.034402 object centre (A): 18.01200 22.56200 67.25450 number of atom coordinates read : 2746 total number of charged atoms : 2597 net assigned charge : 5.039016 assigned positive charge : 421.2159 centred at (gu) : 91.46633 95.34862 92.30564 assigned negative charge : -416.1772 centred at (gu) : 90.52533 94.80670 92.54571 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 90582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23177 grid for indexing accessible points = 1.400000 m= 35109 mr = 64233 m= 6277 mr = 26635 m= 496 mr = 4164 m= 10 mr = 222 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 2940 time to turn everything in is 0.6700000 number of dielectric boundary points 37220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 20550 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) : 0.6781340 object centre at (A) : 18.01200 22.56200 67.25450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8888637E-02 -3.0690970E-02 midg,1,midg; midg,igrid,midg -2.6198025E-03 3.9539728E-02 1,midg,midg; igrid,midg,midg -3.1355988E-02 0.1059002 gauss-seidel spectral radius is 0.9988068 estimated iterations to convergence 229 setup time was (sec) 0.9700000 now iterating at: 15:12:58 rms-change max change #iterations 5.069843 246.7328 at 10iterations 2.481117 79.92889 at 20iterations 1.220388 38.67299 at 30iterations 0.6006110 17.48023 at 40iterations 0.2958976 8.170105 at 50iterations 0.1458044 3.840436 at 60iterations 7.1747668E-02 2.089024 at 70iterations 3.5329979E-02 1.116516 at 80iterations 1.7428756E-02 0.5249023 at 90iterations 8.6106071E-03 0.2341394 at 100iterations 4.2548119E-03 0.1353340 at 110iterations 2.1055401E-03 5.7876587E-02 at 120iterations finished qdiffx linear iterations at : 15:13:05 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 2.1055401E-03 5.7876587E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 15:13:05 7.789u 0.192s 0:08.28 96.2% 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 16 2011 at 15:13:05 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2746 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: SEP 228 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.051603 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): -5.973000 41.99700 ymin,ymax (A): -3.583000 48.70700 zmin,zma (A): 41.00600 93.50300 x,y,z range (A): 47.97000 52.29000 52.49700 scale (grids/A): 3.051603 object centre (A): 18.01200 22.56200 67.25450 number of atom coordinates read : 2746 total number of charged atoms : 2597 net assigned charge : 5.039016 assigned positive charge : 421.2159 centred at (gu) : 92.19916 98.02275 93.45863 assigned negative charge : -416.1772 centred at (gu) : 90.78791 97.21004 93.81835 start vw surface at 0.1600000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 208856 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23177 grid for indexing accessible points = 1.400000 m= 110896 mr = 154423 m= 43465 mr = 92529 m= 11701 mr = 35792 m= 2105 mr = 9039 m= 208 mr = 1462 m= 5 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 9906 time to turn everything in is 1.770000 number of dielectric boundary points 83870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 20776 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) : 2.034402 object centre at (A) : 18.01200 22.56200 67.25450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1154184 -0.3481886 midg,1,midg; midg,igrid,midg 3.5351548E-02 0.1463926 1,midg,midg; igrid,midg,midg -0.3434438 0.9535867 gauss-seidel spectral radius is 0.9992965 estimated iterations to convergence 297 setup time was (sec) 2.080000 now iterating at: 15:13:08 rms-change max change #iterations 11.38941 441.6167 at 10iterations 6.704746 174.5583 at 20iterations 3.947297 70.91751 at 30iterations 2.323428 51.94613 at 40iterations 1.367818 25.04992 at 50iterations 0.8001074 14.20183 at 60iterations 0.4690531 8.138676 at 70iterations 0.2745856 4.564043 at 80iterations 0.1606251 2.805340 at 90iterations 9.4012424E-02 1.612593 at 100iterations 5.4961093E-02 0.9012890 at 110iterations 3.2102562E-02 0.5132561 at 120iterations 1.8837834E-02 0.3242645 at 130iterations 1.1057890E-02 0.1746712 at 140iterations 6.5348889E-03 0.1123314 at 150iterations 3.8796091E-03 6.5093994E-02 at 160iterations 2.3355768E-03 4.6716690E-02 at 170iterations 1.4356720E-03 2.8179169E-02 at 180iterations finished qdiffx linear iterations at : 15:13:18 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 1.4356720E-03 2.8179169E-02 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 15:13:19 12.901u 0.190s 0:13.41 97.6% 0+0k 0+0io 0pf+0w