Tue Oct 11 06:01:25 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 Tue Oct 11 2011 at 06:01:25 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2237 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: 0.7565936 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): 25.87800 72.54000 ymin,ymax (A): -18.53100 28.52200 zmin,zma (A): 4.263000 46.49900 x,y,z range (A): 46.66200 47.05300 42.23600 scale (grids/A): 0.7565936 object centre (A): 49.20900 4.995500 25.38100 number of atom coordinates read : 2237 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 89.09682 90.68510 90.14178 assigned negative charge : -303.7472 centred at (gu) : 89.25050 90.56281 90.20849 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8171 nv = 96 ne = 84 npr = 40679 no. pairs analyzed = 40679 no. exposed pairs = 2545 no. arc points = 17564 no. surface atoms = 866 nbur = 1371 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 695 mr = 4831 m= 6 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1461 ## 143 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8400 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6693854E-07 9.7026039E-08 midg,1,midg; midg,igrid,midg 1.7946926E-08 3.9336510E-07 1,midg,midg; igrid,midg,midg 4.5812146E-07 -1.8847096E-08 gauss-seidel spectral radius is 0.9908829 estimated iterations to convergence 85 setup time was (sec) 0.5500000 now iterating at: 06:01:26 rms-change max change #iterations 0.2629392 33.98021 at 10iterations 3.7894454E-02 5.332435 at 20iterations 5.4812143E-03 0.6958923 at 30iterations 9.0582110E-04 0.1209831 at 40iterations 2.1537593E-04 2.3689270E-02 at 50iterations finished qdiffx linear iterations at : 06:01:29 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 2.1537593E-04 2.3689270E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 06:01:30 3.535u 0.160s 0:04.32 85.4% 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 06:01:30 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2237 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: 2.269781 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): 25.87800 72.54000 ymin,ymax (A): -18.53100 28.52200 zmin,zma (A): 4.263000 46.49900 x,y,z range (A): 46.66200 47.05300 42.23600 scale (grids/A): 2.269781 object centre (A): 49.20900 4.995500 25.38100 number of atom coordinates read : 2237 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 87.29044 92.05519 90.42519 assigned negative charge : -303.7472 centred at (gu) : 87.75169 91.68850 90.62564 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 85317 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17564 grid for indexing accessible points = 1.400000 m= 37525 mr = 61020 m= 8579 mr = 29158 m= 1010 mr = 5952 m= 39 mr = 565 m= 0 mr = 3 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7500000 number of dielectric boundary points 35772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 15371 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) : 0.7565936 object centre at (A) : 49.20900 4.995500 25.38100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7708616E-02 4.3948937E-02 midg,1,midg; midg,igrid,midg 5.7914194E-02 0.1173022 1,midg,midg; igrid,midg,midg 6.6853337E-02 -7.6572135E-02 gauss-seidel spectral radius is 0.9989563 estimated iterations to convergence 245 setup time was (sec) 1.050000 now iterating at: 06:01:31 rms-change max change #iterations 5.117628 202.9791 at 10iterations 2.640235 83.31258 at 20iterations 1.358939 37.20642 at 30iterations 0.7023855 20.61903 at 40iterations 0.3624114 12.24038 at 50iterations 0.1872105 5.381938 at 60iterations 9.6854977E-02 3.130468 at 70iterations 4.9944039E-02 1.379840 at 80iterations 2.5882684E-02 0.7362785 at 90iterations 1.3481433E-02 0.3816910 at 100iterations 7.0249056E-03 0.1985970 at 110iterations 3.6903601E-03 9.9142075E-02 at 120iterations finished qdiffx linear iterations at : 06:01:38 total time elapsed so far: 8.130000 # loops : 120 mean,max change (kT/e) : 3.6903601E-03 9.9142075E-02 energy calculations done at 8.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.330000 DelPhi exited at 06:01:39 8.329u 0.239s 0:08.92 95.8% 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 Tue Oct 11 2011 at 06:01:39 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2237 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: 3.404671 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): 25.87800 72.54000 ymin,ymax (A): -18.53100 28.52200 zmin,zma (A): 4.263000 46.49900 x,y,z range (A): 46.66200 47.05300 42.23600 scale (grids/A): 3.404671 object centre (A): 49.20900 4.995500 25.38100 number of atom coordinates read : 2237 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 85.93575 93.08256 90.63773 assigned negative charge : -303.7472 centred at (gu) : 86.62770 92.53281 90.93848 start vw surface at 0.1500000 fill in re-entrant regions at 0.9800000 boundary points on vw surface= 196407 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17564 grid for indexing accessible points = 1.400000 m= 112472 mr = 146428 m= 50973 mr = 94833 m= 16717 mr = 42689 m= 4056 mr = 13244 m= 601 mr = 3042 m= 40 mr = 405 m= 0 mr = 8 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.250000 number of dielectric boundary points 80617 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.400000 number of grid points assigned charge 15432 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) : 2.269781 object centre at (A) : 49.20900 4.995500 25.38100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1145789 0.3169833 midg,1,midg; midg,igrid,midg 0.4359843 0.8196903 1,midg,midg; igrid,midg,midg 0.5689600 -0.8319179 gauss-seidel spectral radius is 0.9993294 estimated iterations to convergence 305 setup time was (sec) 2.590000 now iterating at: 06:01:42 rms-change max change #iterations 11.02808 378.2520 at 10iterations 6.645842 154.0562 at 20iterations 3.979872 88.65266 at 30iterations 2.380275 45.38427 at 40iterations 1.419397 24.47044 at 50iterations 0.8466277 16.00078 at 60iterations 0.5044626 8.831848 at 70iterations 0.3000156 5.094378 at 80iterations 0.1781217 3.505929 at 90iterations 0.1061457 1.666821 at 100iterations 6.3147537E-02 1.143496 at 110iterations 3.7606031E-02 0.5993195 at 120iterations 2.2584749E-02 0.3518372 at 130iterations 1.3693224E-02 0.2313004 at 140iterations 8.4849559E-03 0.1394958 at 150iterations 5.4539763E-03 9.6397400E-02 at 160iterations 3.6653227E-03 7.4961662E-02 at 170iterations 2.6211496E-03 4.8311234E-02 at 180iterations finished qdiffx linear iterations at : 06:01:52 total time elapsed so far: 13.08000 # loops : 180 mean,max change (kT/e) : 2.6211496E-03 4.8311234E-02 energy calculations done at 13.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.27000 DelPhi exited at 06:01:53 13.271u 0.241s 0:13.87 97.4% 0+0k 0+0io 0pf+0w