Sun Oct 9 04:15:35 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 Sun Oct 9 2011 at 04:15:35 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: 355 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4448 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4363654 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): -3.270000 78.31300 ymin,ymax (A): -10.36900 56.22600 zmin,zma (A): 15.64400 74.17400 x,y,z range (A): 81.58300 66.59500 58.53000 scale (grids/A): 0.4363654 object centre (A): 37.52150 22.92850 44.90900 number of atom coordinates read : 4448 total number of charged atoms : 4211 net assigned charge : 18.91999 assigned positive charge : 658.4347 centred at (gu) : 85.61140 91.38749 88.60892 assigned negative charge : -639.5189 centred at (gu) : 85.47589 91.47184 88.62011 start vw surface at 0.2000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5022 nv = 96 ne = 84 npr = 90476 no. pairs analyzed = 90476 no. exposed pairs = 5671 no. arc points = 39346 no. surface atoms = 1910 nbur = 2538 mkacc time = 0.2000000 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 = 1.932000 m= 125 mr = 2342 m= 0 mr = 1 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 2804 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3216 ## 660 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 6785 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.8475264E-12 3.4890578E-12 midg,1,midg; midg,igrid,midg 6.8558670E-12 1.7319095E-12 1,midg,midg; igrid,midg,midg -7.8937100E-12 3.5673400E-12 gauss-seidel spectral radius is 0.9732000 estimated iterations to convergence 51 setup time was (sec) 0.6500000 now iterating at: 04:15:36 rms-change max change #iterations 3.0562557E-02 5.857975 at 10iterations 3.0920585E-03 0.4647007 at 20iterations 8.9384784E-04 0.1348076 at 30iterations 2.6789689E-04 4.0819168E-02 at 40iterations 8.0318656E-05 1.2332916E-02 at 50iterations finished qdiffx linear iterations at : 04:15:39 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 8.0318656E-05 1.2332916E-02 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 04:15:39 3.474u 0.194s 0:03.95 92.6% 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 Sun Oct 9 2011 at 04:15:39 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: 355 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4448 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.309096 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): -3.270000 78.31300 ymin,ymax (A): -10.36900 56.22600 zmin,zma (A): 15.64400 74.17400 x,y,z range (A): 81.58300 66.59500 58.53000 scale (grids/A): 1.309096 object centre (A): 37.52150 22.92850 44.90900 number of atom coordinates read : 4448 total number of charged atoms : 4211 net assigned charge : 18.91999 assigned positive charge : 658.4347 centred at (gu) : 76.83277 94.16116 85.82523 assigned negative charge : -639.5189 centred at (gu) : 76.42752 94.41493 85.86018 start vw surface at 0.1900000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 57934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39346 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 13497 mr = 37625 m= 670 mr = 8089 m= 10 mr = 140 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 478 time to turn everything in is 0.4700000 number of dielectric boundary points 26257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 664 ## 25 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 29587 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) : 0.4363654 object centre at (A) : 37.52150 22.92850 44.90900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3985290E-03 1.9581651E-03 midg,1,midg; midg,igrid,midg 5.6000226E-03 2.8495388E-03 1,midg,midg; igrid,midg,midg -7.3660915E-03 4.5136162E-03 gauss-seidel spectral radius is 0.9972429 estimated iterations to convergence 152 setup time was (sec) 0.7500000 now iterating at: 04:15:40 rms-change max change #iterations 2.424078 130.4772 at 10iterations 0.8320969 37.33863 at 20iterations 0.2847847 11.49577 at 30iterations 9.8271616E-02 4.147377 at 40iterations 3.3897579E-02 1.470099 at 50iterations 1.2044000E-02 0.5338926 at 60iterations 4.7246609E-03 0.2297525 at 70iterations 2.2396781E-03 9.1554642E-02 at 80iterations 1.2697820E-03 4.6321869E-02 at 90iterations 8.1331428E-04 2.7606487E-02 at 100iterations 5.3739012E-04 1.7759323E-02 at 110iterations 3.5981787E-04 1.2031555E-02 at 120iterations finished qdiffx linear iterations at : 04:15:46 total time elapsed so far: 7.100000 # loops : 120 mean,max change (kT/e) : 3.5981787E-04 1.2031555E-02 energy calculations done at 7.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.280000 DelPhi exited at 04:15:47 7.279u 0.220s 0:07.85 95.4% 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 Sun Oct 9 2011 at 04:15:47 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: 355 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4448 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.963644 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): -3.270000 78.31300 ymin,ymax (A): -10.36900 56.22600 zmin,zma (A): 15.64400 74.17400 x,y,z range (A): 81.58300 66.59500 58.53000 scale (grids/A): 1.963644 object centre (A): 37.52150 22.92850 44.90900 number of atom coordinates read : 4448 total number of charged atoms : 4211 net assigned charge : 18.91999 assigned positive charge : 658.4347 centred at (gu) : 70.24883 96.24151 83.73757 assigned negative charge : -639.5189 centred at (gu) : 69.64114 96.62222 83.79030 start vw surface at 0.1900000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 135585 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39346 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 52301 mr = 93887 m= 9532 mr = 38509 m= 669 mr = 6068 m= 8 mr = 282 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 1510 time to turn everything in is 1.010000 number of dielectric boundary points 59349 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 177 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 33236 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) : 1.309096 object centre at (A) : 37.52150 22.92850 44.90900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1051814 4.6697613E-02 midg,1,midg; midg,igrid,midg 0.1575706 7.8476362E-02 1,midg,midg; igrid,midg,midg -0.1705183 6.1914511E-02 gauss-seidel spectral radius is 0.9988415 estimated iterations to convergence 233 setup time was (sec) 1.320000 now iterating at: 04:15:48 rms-change max change #iterations 7.325922 228.5744 at 10iterations 3.797034 118.9140 at 20iterations 1.953068 51.26205 at 30iterations 0.9982057 27.69095 at 40iterations 0.5087197 12.65556 at 50iterations 0.2574690 7.459827 at 60iterations 0.1304149 3.060799 at 70iterations 6.5541394E-02 1.758818 at 80iterations 3.3045005E-02 0.7936978 at 90iterations 1.6626701E-02 0.4244957 at 100iterations 8.3625000E-03 0.2099609 at 110iterations 4.2254059E-03 0.1076603 at 120iterations 2.1492727E-03 5.3890228E-02 at 130iterations 1.1096736E-03 3.2484055E-02 at 140iterations 5.9087813E-04 1.6132355E-02 at 150iterations 3.3084580E-04 8.1138611E-03 at 160iterations 2.0019434E-04 4.8575401E-03 at 170iterations 1.3096831E-04 2.8705597E-03 at 180iterations finished qdiffx linear iterations at : 04:15:59 total time elapsed so far: 11.33000 # loops : 180 mean,max change (kT/e) : 1.3096831E-04 2.8705597E-03 energy calculations done at 11.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.51000 DelPhi exited at 04:15:59 11.509u 0.215s 0:11.99 97.6% 0+0k 0+0io 0pf+0w