Sun Oct 9 21:01:41 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 Sun Oct 9 2011 at 21:01:41 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2575 !!! WARNING: CYS 261 has a net charge of 0.5000 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: 0.6626831 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): -8.413000 38.49900 ymin,ymax (A): -27.42300 26.29800 zmin,zma (A): -12.73300 40.44700 x,y,z range (A): 46.91199 53.72100 53.18000 scale (grids/A): 0.6626831 object centre (A): 15.04300 -0.5625000 13.85700 number of atom coordinates read : 2575 total number of charged atoms : 2431 net assigned charge : 5.500012 assigned positive charge : 388.4979 centred at (gu) : 89.78886 90.16107 90.29312 assigned negative charge : -382.9987 centred at (gu) : 89.70707 90.13362 90.31782 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7509 nv = 96 ne = 84 npr = 52000 no. pairs analyzed = 52000 no. exposed pairs = 3183 no. arc points = 22680 no. surface atoms = 1088 nbur = 1487 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 433 mr = 4018 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3000000 number of dielectric boundary points 3867 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2252 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8937 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9074996E-08 1.0489314E-08 midg,1,midg; midg,igrid,midg 9.0452428E-09 2.1508253E-08 1,midg,midg; igrid,midg,midg -2.3093056E-09 3.0689716E-08 gauss-seidel spectral radius is 0.9881973 estimated iterations to convergence 75 setup time was (sec) 0.5300000 now iterating at: 21:01:42 rms-change max change #iterations 0.1693679 27.29924 at 10iterations 1.8243957E-02 2.518890 at 20iterations 1.9522141E-03 0.2585649 at 30iterations 2.1015869E-04 3.1425476E-02 at 40iterations 2.2431435E-05 3.0846596E-03 at 50iterations finished qdiffx linear iterations at : 21:01:44 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 2.2431435E-05 3.0846596E-03 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 21:01:45 3.330u 0.153s 0:03.86 90.1% 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 21:01:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2575 !!! WARNING: CYS 261 has a net charge of 0.5000 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: 1.988049 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): -8.413000 38.49900 ymin,ymax (A): -27.42300 26.29800 zmin,zma (A): -12.73300 40.44700 x,y,z range (A): 46.91199 53.72100 53.18000 scale (grids/A): 1.988049 object centre (A): 15.04300 -0.5625000 13.85700 number of atom coordinates read : 2575 total number of charged atoms : 2431 net assigned charge : 5.500012 assigned positive charge : 388.4979 centred at (gu) : 89.36591 90.48233 90.87871 assigned negative charge : -382.9987 centred at (gu) : 89.12099 90.40056 90.95332 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 80664 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22680 grid for indexing accessible points = 1.400000 m= 29027 mr = 55059 m= 4759 mr = 21136 m= 356 mr = 2873 m= 2 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1018 time to turn everything in is 0.5900000 number of dielectric boundary points 35592 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 19225 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) : 0.6626831 object centre at (A) : 15.04300 -0.5625000 13.85700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1567560E-02 -1.5537404E-02 midg,1,midg; midg,igrid,midg 3.9095283E-02 3.5445984E-02 1,midg,midg; igrid,midg,midg -8.3917370E-03 1.6898014E-02 gauss-seidel spectral radius is 0.9987348 estimated iterations to convergence 223 setup time was (sec) 0.8800000 now iterating at: 21:01:46 rms-change max change #iterations 4.556578 188.9457 at 10iterations 2.188941 74.07758 at 20iterations 1.050896 30.04758 at 30iterations 0.5054110 15.30269 at 40iterations 0.2434071 6.979743 at 50iterations 0.1169690 3.414507 at 60iterations 5.6250934E-02 1.643730 at 70iterations 2.7069049E-02 0.8103104 at 80iterations 1.3039351E-02 0.4393539 at 90iterations 6.2901415E-03 0.1965027 at 100iterations 3.0226801E-03 9.5367432E-02 at 110iterations 1.4568460E-03 4.3305397E-02 at 120iterations finished qdiffx linear iterations at : 21:01:52 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 1.4568460E-03 4.3305397E-02 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.480000 DelPhi exited at 21:01:53 7.483u 0.150s 0:07.95 95.9% 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 21:01:53 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2575 !!! WARNING: CYS 261 has a net charge of 0.5000 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: 2.982074 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): -8.413000 38.49900 ymin,ymax (A): -27.42300 26.29800 zmin,zma (A): -12.73300 40.44700 x,y,z range (A): 46.91199 53.72100 53.18000 scale (grids/A): 2.982074 object centre (A): 15.04300 -0.5625000 13.85700 number of atom coordinates read : 2575 total number of charged atoms : 2431 net assigned charge : 5.500012 assigned positive charge : 388.4979 centred at (gu) : 89.04870 90.72349 91.31819 assigned negative charge : -382.9987 centred at (gu) : 88.68150 90.60099 91.43001 start vw surface at 0.1400000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 186325 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22680 grid for indexing accessible points = 1.400000 m= 92985 mr = 133227 m= 34382 mr = 75672 m= 8678 mr = 27423 m= 1457 mr = 6328 m= 102 mr = 960 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 3269 time to turn everything in is 1.510000 number of dielectric boundary points 80280 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 19447 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) : 1.988049 object centre at (A) : 15.04300 -0.5625000 13.85700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2876096 -0.3344986 midg,1,midg; midg,igrid,midg 0.5056802 0.4420195 1,midg,midg; igrid,midg,midg -7.2292030E-02 0.1441602 gauss-seidel spectral radius is 0.9992880 estimated iterations to convergence 296 setup time was (sec) 1.810000 now iterating at: 21:01:55 rms-change max change #iterations 10.47478 330.3807 at 10iterations 6.149909 132.0806 at 20iterations 3.590245 75.12463 at 30iterations 2.095963 41.25150 at 40iterations 1.221719 21.09183 at 50iterations 0.7097203 13.03311 at 60iterations 0.4129879 7.158715 at 70iterations 0.2404058 4.005508 at 80iterations 0.1390577 2.541960 at 90iterations 8.0789663E-02 1.585814 at 100iterations 4.7035199E-02 0.7924728 at 110iterations 2.7272247E-02 0.4841256 at 120iterations 1.5812907E-02 0.2620220 at 130iterations 9.1732666E-03 0.1513290 at 140iterations 5.3253765E-03 9.9536896E-02 at 150iterations 3.0895644E-03 4.9838066E-02 at 160iterations 1.7934663E-03 3.0075073E-02 at 170iterations 1.0407314E-03 1.7667770E-02 at 180iterations finished qdiffx linear iterations at : 21:02:06 total time elapsed so far: 13.04000 # loops : 180 mean,max change (kT/e) : 1.0407314E-03 1.7667770E-02 energy calculations done at 13.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.26000 DelPhi exited at 21:02:06 13.260u 0.180s 0:13.72 97.9% 0+0k 0+0io 0pf+0w