Tue Oct 11 08:35:04 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 08:35:04 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2057 !!! 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7446453 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): -4.238000 43.57000 ymin,ymax (A): -21.90800 25.51600 zmin,zma (A): 6.070000 48.38900 x,y,z range (A): 47.80800 47.42400 42.31900 scale (grids/A): 0.7446453 object centre (A): 19.66600 1.803999 27.22950 number of atom coordinates read : 2057 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 312.5571 centred at (gu) : 90.98074 88.90187 90.01764 assigned negative charge : -305.6262 centred at (gu) : 90.84153 89.01659 89.98350 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7783 nv = 96 ne = 84 npr = 41751 no. pairs analyzed = 41751 no. exposed pairs = 2415 no. arc points = 16961 no. surface atoms = 822 nbur = 1235 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 541 mr = 4554 m= 6 mr = 100 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 0.2500000 number of dielectric boundary points 3676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1456 ## 136 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8234 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5073652E-08 1.6859779E-07 midg,1,midg; midg,igrid,midg 3.0981519E-07 8.2281044E-09 1,midg,midg; igrid,midg,midg -1.3912415E-08 3.3380502E-07 gauss-seidel spectral radius is 0.9905879 estimated iterations to convergence 84 setup time was (sec) 0.5600000 now iterating at: 08:35:05 rms-change max change #iterations 0.2517841 37.95326 at 10iterations 3.4322269E-02 4.341440 at 20iterations 4.9808151E-03 0.5742087 at 30iterations 8.1745314E-04 0.1180267 at 40iterations 1.7857944E-04 2.2205353E-02 at 50iterations finished qdiffx linear iterations at : 08:35:09 total time elapsed so far: 4.590000 # loops : 50 mean,max change (kT/e) : 1.7857944E-04 2.2205353E-02 energy calculations done at 4.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.750000 DelPhi exited at 08:35:10 4.757u 0.373s 0:05.66 90.4% 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 08:35:10 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2057 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.233936 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): -4.238000 43.57000 ymin,ymax (A): -21.90800 25.51600 zmin,zma (A): 6.070000 48.38900 x,y,z range (A): 47.80800 47.42400 42.31900 scale (grids/A): 2.233936 object centre (A): 19.66600 1.803999 27.22950 number of atom coordinates read : 2057 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 312.5571 centred at (gu) : 92.94231 86.70580 90.05309 assigned negative charge : -305.6262 centred at (gu) : 92.52470 87.04984 89.95056 start vw surface at 0.1000000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 82021 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16961 grid for indexing accessible points = 1.400000 m= 34399 mr = 58866 m= 7331 mr = 26556 m= 806 mr = 5022 m= 25 mr = 412 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 33726 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 15288 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) : 0.7446453 object centre at (A) : 19.66600 1.803999 27.22950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2049034E-02 2.5629433E-02 midg,1,midg; midg,igrid,midg 4.7224071E-02 -4.8503019E-02 1,midg,midg; igrid,midg,midg 5.6497514E-02 0.1306512 gauss-seidel spectral radius is 0.9989248 estimated iterations to convergence 241 setup time was (sec) 0.9900000 now iterating at: 08:35:11 rms-change max change #iterations 5.042803 212.2582 at 10iterations 2.566433 86.96396 at 20iterations 1.314280 41.49659 at 30iterations 0.6704811 19.51643 at 40iterations 0.3428136 10.23862 at 50iterations 0.1750512 4.949255 at 60iterations 8.9392409E-02 2.451169 at 70iterations 4.5787454E-02 1.332836 at 80iterations 2.3531055E-02 0.6918449 at 90iterations 1.2140681E-02 0.3233337 at 100iterations 6.2717171E-03 0.1793437 at 110iterations 3.2643911E-03 9.3439102E-02 at 120iterations finished qdiffx linear iterations at : 08:35:22 total time elapsed so far: 12.08000 # loops : 120 mean,max change (kT/e) : 3.2643911E-03 9.3439102E-02 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.26000 DelPhi exited at 08:35:23 12.264u 0.445s 0:13.14 96.6% 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 08:35:23 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2057 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.350904 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): -4.238000 43.57000 ymin,ymax (A): -21.90800 25.51600 zmin,zma (A): 6.070000 48.38900 x,y,z range (A): 47.80800 47.42400 42.31900 scale (grids/A): 3.350904 object centre (A): 19.66600 1.803999 27.22950 number of atom coordinates read : 2057 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 312.5571 centred at (gu) : 94.41340 85.05873 90.07966 assigned negative charge : -305.6262 centred at (gu) : 93.78713 85.57482 89.92597 start vw surface at 0.1200000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 188829 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16961 grid for indexing accessible points = 1.400000 m= 105339 mr = 141164 m= 45124 mr = 88610 m= 14084 mr = 37670 m= 3174 mr = 10921 m= 488 mr = 2325 m= 23 mr = 332 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.200000 number of dielectric boundary points 76034 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 15384 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) : 2.233936 object centre at (A) : 19.66600 1.803999 27.22950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2119629 0.1056139 midg,1,midg; midg,igrid,midg 0.3952135 -0.6071757 1,midg,midg; igrid,midg,midg 0.5142249 1.049590 gauss-seidel spectral radius is 0.9993203 estimated iterations to convergence 303 setup time was (sec) 2.600000 now iterating at: 08:35:26 rms-change max change #iterations 10.95146 354.8588 at 10iterations 6.552933 128.0542 at 20iterations 3.906423 73.17129 at 30iterations 2.327048 48.29637 at 40iterations 1.381461 25.58617 at 50iterations 0.8189798 13.67799 at 60iterations 0.4856054 8.540115 at 70iterations 0.2872366 4.575016 at 80iterations 0.1701991 2.772961 at 90iterations 0.1005931 1.584167 at 100iterations 5.9729416E-02 1.002108 at 110iterations 3.5568371E-02 0.5673103 at 120iterations 2.1359969E-02 0.3651695 at 130iterations 1.2974815E-02 0.2094193 at 140iterations 8.1014456E-03 0.1587219 at 150iterations 5.2486775E-03 0.1062698 at 160iterations 3.5661159E-03 6.6806793E-02 at 170iterations 2.5750550E-03 4.9442291E-02 at 180iterations finished qdiffx linear iterations at : 08:35:43 total time elapsed so far: 20.01000 # loops : 180 mean,max change (kT/e) : 2.5750550E-03 4.9442291E-02 energy calculations done at 20.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.18000 DelPhi exited at 08:35:44 20.183u 0.443s 0:20.97 98.3% 0+0k 0+0io 0pf+0w