Tue Oct 11 06:10:35 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 Tue Oct 11 2011 at 06:10:35 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2209 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7157937 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): 2.629000 47.58400 ymin,ymax (A): 1.871000 40.71700 zmin,zma (A): -2.759000 46.97600 x,y,z range (A): 44.95500 38.84600 49.73500 scale (grids/A): 0.7157937 object centre (A): 25.10650 21.29400 22.10850 number of atom coordinates read : 2209 total number of charged atoms : 1931 net assigned charge : 6.931010 assigned positive charge : 313.1771 centred at (gu) : 90.17448 90.30735 90.52748 assigned negative charge : -306.2461 centred at (gu) : 90.36434 90.29443 90.54263 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7086 nv = 96 ne = 84 npr = 39759 no. pairs analyzed = 39759 no. exposed pairs = 2437 no. arc points = 16994 no. surface atoms = 834 nbur = 1375 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 471 mr = 4046 m= 3 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3430 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1624 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7827 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2747639E-08 6.8994332E-08 midg,1,midg; midg,igrid,midg 6.0381076E-08 8.3652218E-08 1,midg,midg; igrid,midg,midg 1.7422587E-07 -4.3072610E-08 gauss-seidel spectral radius is 0.9898188 estimated iterations to convergence 81 setup time was (sec) 0.5300000 now iterating at: 06:10:36 rms-change max change #iterations 0.2081012 28.57633 at 10iterations 2.6782135E-02 4.259537 at 20iterations 3.5310006E-03 0.4895248 at 30iterations 5.2880211E-04 6.9410324E-02 at 40iterations 1.1515224E-04 1.6784668E-02 at 50iterations finished qdiffx linear iterations at : 06:10:39 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 1.1515224E-04 1.6784668E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 06:10:39 3.545u 0.202s 0:04.12 90.7% 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 Tue Oct 11 2011 at 06:10:39 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2209 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.147381 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): 2.629000 47.58400 ymin,ymax (A): 1.871000 40.71700 zmin,zma (A): -2.759000 46.97600 x,y,z range (A): 44.95500 38.84600 49.73500 scale (grids/A): 2.147381 object centre (A): 25.10650 21.29400 22.10850 number of atom coordinates read : 2209 total number of charged atoms : 1931 net assigned charge : 6.931010 assigned positive charge : 313.1771 centred at (gu) : 90.52341 90.92218 91.58232 assigned negative charge : -306.2461 centred at (gu) : 91.09303 90.88348 91.62779 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 75250 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16994 grid for indexing accessible points = 1.400000 m= 30396 mr = 53498 m= 5868 mr = 23164 m= 552 mr = 3859 m= 11 mr = 307 m= 0 mr = 2 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 31247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 46 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15232 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) : 0.7157937 object centre at (A) : 25.10650 21.29400 22.10850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6647523E-02 6.6685654E-02 midg,1,midg; midg,igrid,midg 4.1841953E-03 3.2542441E-02 1,midg,midg; igrid,midg,midg 4.3981932E-02 3.9979257E-03 gauss-seidel spectral radius is 0.9988498 estimated iterations to convergence 233 setup time was (sec) 0.9400000 now iterating at: 06:10:41 rms-change max change #iterations 4.673045 179.5324 at 10iterations 2.319306 78.03088 at 20iterations 1.158871 37.27914 at 30iterations 0.5767702 17.23469 at 40iterations 0.2901511 8.959771 at 50iterations 0.1444506 4.371537 at 60iterations 7.2193578E-02 2.622383 at 70iterations 3.6098942E-02 1.134248 at 80iterations 1.8130271E-02 0.5305057 at 90iterations 9.1452990E-03 0.2834072 at 100iterations 4.6255994E-03 0.1315670 at 110iterations 2.3696860E-03 7.6284409E-02 at 120iterations finished qdiffx linear iterations at : 06:10:48 total time elapsed so far: 8.200000 # loops : 120 mean,max change (kT/e) : 2.3696860E-03 7.6284409E-02 energy calculations done at 8.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.390000 DelPhi exited at 06:10:48 8.390u 0.278s 0:08.98 96.4% 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 Tue Oct 11 2011 at 06:10:48 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2209 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.221072 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): 2.629000 47.58400 ymin,ymax (A): 1.871000 40.71700 zmin,zma (A): -2.759000 46.97600 x,y,z range (A): 44.95500 38.84600 49.73500 scale (grids/A): 3.221072 object centre (A): 25.10650 21.29400 22.10850 number of atom coordinates read : 2209 total number of charged atoms : 1931 net assigned charge : 6.931010 assigned positive charge : 313.1771 centred at (gu) : 90.78520 91.38333 92.37347 assigned negative charge : -306.2461 centred at (gu) : 91.63951 91.32528 92.44189 start vw surface at 0.1500000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 173382 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16994 grid for indexing accessible points = 1.400000 m= 94817 mr = 128888 m= 38512 mr = 79081 m= 11125 mr = 31530 m= 2278 mr = 8614 m= 268 mr = 1649 m= 3 mr = 195 m= 0 mr = 2 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.940000 number of dielectric boundary points 70426 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 15448 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) : 2.147381 object centre at (A) : 25.10650 21.29400 22.10850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4315009 0.6203234 midg,1,midg; midg,igrid,midg 5.6833150E-03 0.2516166 1,midg,midg; igrid,midg,midg 0.3423432 9.8750226E-02 gauss-seidel spectral radius is 0.9992993 estimated iterations to convergence 298 setup time was (sec) 2.250000 now iterating at: 06:10:51 rms-change max change #iterations 10.41816 389.5369 at 10iterations 6.171036 149.4225 at 20iterations 3.654117 87.16758 at 30iterations 2.160123 50.34212 at 40iterations 1.272080 24.25706 at 50iterations 0.7472403 15.50594 at 60iterations 0.4404847 8.455035 at 70iterations 0.2594302 4.871058 at 80iterations 0.1519144 2.945790 at 90iterations 8.9363620E-02 1.546764 at 100iterations 5.2523676E-02 0.9603424 at 110iterations 3.0981410E-02 0.5822277 at 120iterations 1.8370656E-02 0.3285317 at 130iterations 1.1003979E-02 0.2054310 at 140iterations 6.7360522E-03 0.1249657 at 150iterations 4.2408318E-03 8.0610275E-02 at 160iterations 2.8145441E-03 5.7903290E-02 at 170iterations 1.9662958E-03 3.7130356E-02 at 180iterations finished qdiffx linear iterations at : 06:11:01 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 1.9662958E-03 3.7130356E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 06:11:02 12.876u 0.255s 0:13.53 96.9% 0+0k 0+0io 0pf+0w