Tue Oct 11 08:12:19 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 08:12:19 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 = 2647 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6105927 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): 10.19100 64.62300 ymin,ymax (A): -1.498000 56.80600 zmin,zma (A): 10.27200 53.12600 x,y,z range (A): 54.43200 58.30400 42.85400 scale (grids/A): 0.6105927 object centre (A): 37.40700 27.65400 31.69900 number of atom coordinates read : 2647 total number of charged atoms : 2506 net assigned charge : 9.000021 assigned positive charge : 398.8087 centred at (gu) : 88.66362 91.34494 89.94620 assigned negative charge : -389.8094 centred at (gu) : 88.65530 91.13464 90.07932 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6536 nv = 96 ne = 84 npr = 53183 no. pairs analyzed = 53183 no. exposed pairs = 3179 no. arc points = 22276 no. surface atoms = 1069 nbur = 1578 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 327 mr = 3675 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 70 time to turn everything in is 0.3000000 number of dielectric boundary points 3151 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2218 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8082 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2008466E-08 -1.5444216E-09 midg,1,midg; midg,igrid,midg -4.0787418E-09 2.1134097E-08 1,midg,midg; igrid,midg,midg 6.4491514E-09 4.2559445E-09 gauss-seidel spectral radius is 0.9861148 estimated iterations to convergence 70 setup time was (sec) 0.5100000 now iterating at: 08:12:20 rms-change max change #iterations 0.1197682 18.45011 at 10iterations 1.1995601E-02 2.130161 at 20iterations 1.6918407E-03 0.3336792 at 30iterations 4.1157595E-04 9.3898773E-02 at 40iterations 1.1729873E-04 2.7397156E-02 at 50iterations finished qdiffx linear iterations at : 08:12:22 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 1.1729873E-04 2.7397156E-02 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 08:12:22 3.113u 0.151s 0:03.57 91.3% 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 08:12:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2647 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: 1.831778 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): 10.19100 64.62300 ymin,ymax (A): -1.498000 56.80600 zmin,zma (A): 10.27200 53.12600 x,y,z range (A): 54.43200 58.30400 42.85400 scale (grids/A): 1.831778 object centre (A): 37.40700 27.65400 31.69900 number of atom coordinates read : 2647 total number of charged atoms : 2506 net assigned charge : 9.000021 assigned positive charge : 398.8087 centred at (gu) : 85.99020 94.03448 89.83811 assigned negative charge : -389.8094 centred at (gu) : 85.96562 93.40376 90.23755 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70979 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22276 grid for indexing accessible points = 1.400000 m= 25201 mr = 49867 m= 3515 mr = 18789 m= 141 mr = 2171 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 2262 time to turn everything in is 0.4900000 number of dielectric boundary points 28976 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 173 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 19611 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) : 0.6105927 object centre at (A) : 37.40700 27.65400 31.69900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0498061E-02 5.9971847E-03 midg,1,midg; midg,igrid,midg -2.6364224E-02 2.3174416E-02 1,midg,midg; igrid,midg,midg 9.0402889E-04 1.7740661E-02 gauss-seidel spectral radius is 0.9985265 estimated iterations to convergence 207 setup time was (sec) 0.7500000 now iterating at: 08:12:23 rms-change max change #iterations 3.950300 163.0626 at 10iterations 1.782940 67.07478 at 20iterations 0.8118004 25.83531 at 30iterations 0.3674816 13.41234 at 40iterations 0.1684786 5.692715 at 50iterations 7.7256367E-02 2.439512 at 60iterations 3.5288103E-02 1.080740 at 70iterations 1.6164899E-02 0.5019684 at 80iterations 7.5328220E-03 0.2325516 at 90iterations 3.5914527E-03 0.1216278 at 100iterations 1.7891899E-03 6.6505432E-02 at 110iterations 9.3677681E-04 4.0000916E-02 at 120iterations finished qdiffx linear iterations at : 08:12:29 total time elapsed so far: 6.670000 # loops : 120 mean,max change (kT/e) : 9.3677681E-04 4.0000916E-02 energy calculations done at 6.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.840000 DelPhi exited at 08:12:30 6.843u 0.170s 0:07.40 94.7% 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 08:12:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2647 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: 2.747667 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): 10.19100 64.62300 ymin,ymax (A): -1.498000 56.80600 zmin,zma (A): 10.27200 53.12600 x,y,z range (A): 54.43200 58.30400 42.85400 scale (grids/A): 2.747667 object centre (A): 37.40700 27.65400 31.69900 number of atom coordinates read : 2647 total number of charged atoms : 2506 net assigned charge : 9.000021 assigned positive charge : 398.8087 centred at (gu) : 83.98496 96.05154 89.75695 assigned negative charge : -389.8094 centred at (gu) : 83.94839 95.10561 90.35617 start vw surface at 0.1300000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 164630 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22276 grid for indexing accessible points = 1.400000 m= 82468 mr = 120833 m= 28746 mr = 67878 m= 6123 mr = 23340 m= 616 mr = 4613 m= 18 mr = 401 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 7423 time to turn everything in is 1.170000 number of dielectric boundary points 65530 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 20047 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) : 1.831778 object centre at (A) : 37.40700 27.65400 31.69900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3378838 9.0034984E-02 midg,1,midg; midg,igrid,midg -0.4495780 -6.9461986E-02 1,midg,midg; igrid,midg,midg -6.7256153E-02 0.1189026 gauss-seidel spectral radius is 0.9992238 estimated iterations to convergence 283 setup time was (sec) 1.440000 now iterating at: 08:12:32 rms-change max change #iterations 9.296104 379.5970 at 10iterations 5.325453 111.0119 at 20iterations 3.030027 60.40924 at 30iterations 1.721741 33.25306 at 40iterations 0.9772668 18.17328 at 50iterations 0.5555124 10.46375 at 60iterations 0.3151537 5.851551 at 70iterations 0.1786953 3.429504 at 80iterations 0.1015851 2.035906 at 90iterations 5.7787277E-02 1.139209 at 100iterations 3.2891445E-02 0.6036491 at 110iterations 1.8821329E-02 0.3774338 at 120iterations 1.0847514E-02 0.2184601 at 130iterations 6.3540130E-03 0.1296272 at 140iterations 3.7997514E-03 8.3515167E-02 at 150iterations 2.3627107E-03 5.2352905E-02 at 160iterations 1.5477466E-03 3.6430359E-02 at 170iterations 1.0683680E-03 2.5714874E-02 at 180iterations finished qdiffx linear iterations at : 08:12:41 total time elapsed so far: 10.80000 # loops : 180 mean,max change (kT/e) : 1.0683680E-03 2.5714874E-02 energy calculations done at 10.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.02000 DelPhi exited at 08:12:42 11.020u 0.200s 0:11.61 96.6% 0+0k 0+0io 0pf+0w