Sat Oct 8 17:05:29 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 Sat Oct 8 2011 at 17:05:29 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3683 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5387002 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): -28.31500 31.94600 ymin,ymax (A): -34.14500 31.94000 zmin,zma (A): 9.012000 63.78900 x,y,z range (A): 60.26100 66.08500 54.77700 scale (grids/A): 0.5387002 object centre (A): 1.815499 -1.102498 36.40050 number of atom coordinates read : 3683 total number of charged atoms : 3534 net assigned charge : -8.999981 assigned positive charge : 563.3948 centred at (gu) : 89.26400 90.22654 90.71064 assigned negative charge : -572.3969 centred at (gu) : 89.33258 90.24369 90.72868 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6838 nv = 96 ne = 84 npr = 75054 no. pairs analyzed = 75054 no. exposed pairs = 4484 no. arc points = 31485 no. surface atoms = 1515 nbur = 2168 mkacc time = 0.2100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 274 mr = 3637 m= 0 mr = 21 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 3454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3158 ## 410 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 9038 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5769786E-10 -6.4270389E-10 midg,1,midg; midg,igrid,midg -2.9449823E-10 -5.6407995E-10 1,midg,midg; igrid,midg,midg 2.7685437E-11 -7.2554496E-10 gauss-seidel spectral radius is 0.9822871 estimated iterations to convergence 62 setup time was (sec) 0.7200000 now iterating at: 17:05:30 rms-change max change #iterations 7.9811923E-02 12.16917 at 10iterations 5.1915506E-03 0.7261810 at 20iterations 3.5706742E-04 6.3776016E-02 at 30iterations 3.7242964E-05 6.4744949E-03 at 40iterations 8.1717290E-06 1.8258095E-03 at 50iterations finished qdiffx linear iterations at : 17:05:33 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 8.1717290E-06 1.8258095E-03 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.260000 DelPhi exited at 17:05:33 4.267u 0.282s 0:04.88 93.0% 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 Sat Oct 8 2011 at 17:05:34 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3683 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.616101 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): -28.31500 31.94600 ymin,ymax (A): -34.14500 31.94000 zmin,zma (A): 9.012000 63.78900 x,y,z range (A): 60.26100 66.08500 54.77700 scale (grids/A): 1.616101 object centre (A): 1.815499 -1.102498 36.40050 number of atom coordinates read : 3683 total number of charged atoms : 3534 net assigned charge : -8.999981 assigned positive charge : 563.3948 centred at (gu) : 87.79104 90.67858 92.13089 assigned negative charge : -572.3969 centred at (gu) : 87.99722 90.73064 92.18541 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 76319 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31485 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 23576 mr = 53041 m= 2445 mr = 16138 m= 71 mr = 1256 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 340 time to turn everything in is 0.6900000 number of dielectric boundary points 31972 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 409 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 26958 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) : 0.5387002 object centre at (A) : 1.815499 -1.102498 36.40050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9715338E-05 -6.8070050E-03 midg,1,midg; midg,igrid,midg -1.0339174E-03 -1.0944858E-02 1,midg,midg; igrid,midg,midg -1.3776130E-02 -3.1655896E-02 gauss-seidel spectral radius is 0.9982113 estimated iterations to convergence 188 setup time was (sec) 0.9800000 now iterating at: 17:05:35 rms-change max change #iterations 3.763803 190.4667 at 10iterations 1.575183 58.64354 at 20iterations 0.6584989 19.82761 at 30iterations 0.2776542 10.14021 at 40iterations 0.1166856 4.055477 at 50iterations 4.9081419E-02 1.677032 at 60iterations 2.0660374E-02 0.7271118 at 70iterations 8.6712213E-03 0.3086305 at 80iterations 3.6613280E-03 0.1245146 at 90iterations 1.5366537E-03 5.1521301E-02 at 100iterations 6.5115362E-04 2.0720005E-02 at 110iterations 2.7750686E-04 8.8138580E-03 at 120iterations finished qdiffx linear iterations at : 17:05:43 total time elapsed so far: 9.510000 # loops : 120 mean,max change (kT/e) : 2.7750686E-04 8.8138580E-03 energy calculations done at 9.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.690000 DelPhi exited at 17:05:44 9.693u 0.325s 0:10.27 97.4% 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 Sat Oct 8 2011 at 17:05:44 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3683 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.424151 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): -28.31500 31.94600 ymin,ymax (A): -34.14500 31.94000 zmin,zma (A): 9.012000 63.78900 x,y,z range (A): 60.26100 66.08500 54.77700 scale (grids/A): 2.424151 object centre (A): 1.815499 -1.102498 36.40050 number of atom coordinates read : 3683 total number of charged atoms : 3534 net assigned charge : -8.999981 assigned positive charge : 563.3948 centred at (gu) : 86.68629 91.01752 93.19611 assigned negative charge : -572.3969 centred at (gu) : 86.99588 91.09592 93.27798 start vw surface at 0.1800000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 177504 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31485 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 82742 mr = 129623 m= 22975 mr = 65712 m= 3871 mr = 17332 m= 261 mr = 2538 m= 6 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 1158 time to turn everything in is 1.680000 number of dielectric boundary points 72060 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 28228 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) : 1.616101 object centre at (A) : 1.815499 -1.102498 36.40050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4709539E-02 -0.1306531 midg,1,midg; midg,igrid,midg 1.1946885E-02 -8.0644161E-02 1,midg,midg; igrid,midg,midg -0.3210285 -0.4867779 gauss-seidel spectral radius is 0.9991570 estimated iterations to convergence 272 setup time was (sec) 2.010000 now iterating at: 17:05:46 rms-change max change #iterations 9.672279 292.5909 at 10iterations 5.443656 120.4437 at 20iterations 3.064090 79.22646 at 30iterations 1.715117 36.77202 at 40iterations 0.9544486 19.06876 at 50iterations 0.5313507 10.05661 at 60iterations 0.2962222 5.742931 at 70iterations 0.1645779 3.367287 at 80iterations 9.1250032E-02 1.819613 at 90iterations 5.0614621E-02 1.030935 at 100iterations 2.8069835E-02 0.5367575 at 110iterations 1.5516955E-02 0.3052406 at 120iterations 8.6362334E-03 0.1832914 at 130iterations 4.7838502E-03 8.5617065E-02 at 140iterations 2.6606922E-03 5.1282883E-02 at 150iterations 1.4825725E-03 3.0313969E-02 at 160iterations 8.2825782E-04 1.7888069E-02 at 170iterations 4.6928515E-04 9.8247528E-03 at 180iterations finished qdiffx linear iterations at : 17:06:00 total time elapsed so far: 16.16000 # loops : 180 mean,max change (kT/e) : 4.6928515E-04 9.8247528E-03 energy calculations done at 16.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.33000 DelPhi exited at 17:06:01 16.336u 0.361s 0:16.95 98.4% 0+0k 0+0io 0pf+0w